Falconer Biology Library Feed

Library catalogs

mnewman@stanford.edu — Mon, 23 Nov 2009 17:15:59 -0800

Socrates: Stanford's Online Catalog
The catalog of books, journals, digital books and journals, and other materials in the libraries at Stanford.

SearchWorks
SULAIR’s next-generation library catalog.

WorldCat
Books, journals, and other materials in libraries worldwide.

Falconer Biology Library

Books and E-books for BIO 104/200

mnewman@stanford.edu — Mon, 23 Nov 2009 17:05:14 -0800

Books and E-books for BIO 104/200

Falconer Biology Library

Protocols and Encyclopedias

mnewman@stanford.edu — Mon, 23 Nov 2009 16:47:16 -0800

Protocols and Encyclopedias for BIO 104/200

Falconer Biology Library

Molecular Biology Data for BIO 104/200

mnewman@stanford.edu — Mon, 23 Nov 2009 10:44:49 -0800

Molecular Biology Data for BIO 104/200

Falconer Biology Library

CRISP replaced by RePORTER

mnewman@stanford.edu — Thu, 19 Nov 2009 10:07:00 -0800

The familiar CRISP (Computer Retrieval of Information on Scientific Projects) system has been replaced by the RePORT Expenditures and Results (RePORTER) query tool.

Falconer Biology Library

BIO 104/200 Course Guide

mnewman@stanford.edu — Tue, 17 Nov 2009 13:07:04 -0800

Course guide for BIO 104/200

Falconer Biology Library

BIO 104/200 Journals

mnewman@stanford.edu — Tue, 17 Nov 2009 12:53:45 -0800

Journal blocks test

Falconer Biology Library

Falconer Biology Library Course Reserve Request

nmayo@stanford.edu — Tue, 17 Nov 2009 10:55:12 -0800

Please complete the fields below to submit your reserve request. If you have more than 10 titles, submit an additional form. If you need to put personal items on reserve, please bring them to the library instead of listing them here. Email falconerlibrary@stanford.edu if you have any questions or encounter problems with the form.

Falconer Biology Library

Journal Article Alerting Services in Biology

mnewman@stanford.edu — Fri, 13 Nov 2009 13:32:46 -0800

Create alerts and receive weekly updates showing new items that match your search criteria. Set up alerts for topics, authors, or articles that cite a published work. Below is a short list of useful alerting services for biology.

BIOSIS
BIOSIS indexes journal articles, meeting abstracts, and other literature in the life sciences. Enter a search, then select Search History to create an alert. Select My Saved Searches to view previously created alerts. Alerts can be delivered via email or RSS.

PubMed

Falconer Biology Library

Other Data Sources for BIO 104/200

mnewman@stanford.edu — Fri, 13 Nov 2009 13:28:51 -0800

Falconer Biology Library

Rat Genome Database

mnewman@stanford.edu — Fri, 13 Nov 2009 13:25:29 -0800

The Rat Genome Database is a collaborative effort between leading research institutions involved in rat genetic and genomic research.

Falconer Biology Library

Directories of Molecular Biology Sites

mnewman@stanford.edu — Fri, 13 Nov 2009 13:12:12 -0800

Nucleic Acids Research

The NAR Database Issue, published each January, describes molecular biology databases.

Stanford Genomic Resources

Links to systematic analysis projects, resources, laboratories, and departments at Stanford University.

Falconer Biology Library

Selected NCBI Resources

mnewman@stanford.edu — Fri, 13 Nov 2009 13:07:37 -0800

National Center for Biotechnology Information selected resources.

Falconer Biology Library

Entrez Cross-database Search Page

mnewman@stanford.edu — Fri, 13 Nov 2009 12:33:47 -0800

The Entrez Cross-database Search Page lists, describes, and provides a link to each NCBI database. On this page, all NCBI databases can be searched simultaneously.

Falconer Biology Library

EMBL/EBI Resources

mnewman@stanford.edu — Fri, 13 Nov 2009 11:28:18 -0800

Selected resources from the European Molecular Biology Laboratory (EMBL) and European Bioinformatics Institute (EBI).

Falconer Biology Library

Protein Data Bank in Europe (PDBe)

mnewman@stanford.edu — Fri, 13 Nov 2009 11:13:39 -0800

PDBe is the EBI Protein Structure Database in Europe, a project for the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB).

Falconer Biology Library

Ensembl

mnewman@stanford.edu — Fri, 13 Nov 2009 11:09:11 -0800

The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.

Falconer Biology Library

UniProt

mnewman@stanford.edu — Fri, 13 Nov 2009 11:06:13 -0800

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).

Falconer Biology Library

EMBL-Bank

mnewman@stanford.edu — Fri, 13 Nov 2009 11:02:23 -0800

The EMBL Nucleotide Sequence Database, also known as EMBL-Bank, constitutes Europe's primary nucleotide sequence resource.

Falconer Biology Library

European Molecular Biology Laboratory (EMBL)

mnewman@stanford.edu — Fri, 13 Nov 2009 10:53:26 -0800

The European Molecular Biology Laboratory (EMBL) is dedicated to basic research in the molecular life sciences.

Falconer Biology Library

Methods and Research Protocols in Biology

mnewman@stanford.edu — Thu, 12 Nov 2009 14:09:29 -0800

Falconer Biology Library

Nature Protocols

mnewman@stanford.edu — Thu, 12 Nov 2009 14:07:43 -0800

Nature Protocols is an online resource for protocols, including authoritative, peer-reviewed protocols and an interactive Protocols Network.

Falconer Biology Library

Current Protocols in Molecular Biology

mnewman@stanford.edu — Thu, 12 Nov 2009 14:06:35 -0800

Current Protocols in Molecular Biology describes more than 1,000 procedures from hundreds of biologists around the globe.

Falconer Biology Library

Current Protocols

mnewman@stanford.edu — Thu, 12 Nov 2009 14:02:25 -0800

In addition to molecular biology, the Current Protocols series covers bioinformatics, cell biology, human genetics, nucleic acid chemistry, and other areas of chemistry and biology.

Falconer Biology Library

Cold Spring Harbor Protocols

mnewman@stanford.edu — Thu, 12 Nov 2009 14:00:20 -0800

Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging.

Falconer Biology Library

Encyclopedias for BIO 104/200

mnewman@stanford.edu — Thu, 12 Nov 2009 13:31:33 -0800

Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics

Encyclopedia of Life Sciences

Encyclopedia of Molecular Biology

Falconer Biology Library

Research Guides for BIO 104/200

mnewman@stanford.edu — Wed, 11 Nov 2009 10:42:01 -0800

All research guides

Cell Biology Research Guide

Genetics and Genomics Research Guide

Nucleic Acid Analysis Research Guide

Protein Analysis Research Guide

Falconer Biology Library

Browse Key Molecular Biology Subjects in Socrates

mnewman@stanford.edu — Wed, 11 Nov 2009 10:29:13 -0800

DNA repair

DNA replication

DNA transcription

Falconer Biology Library

RefWorks and EndNote

mnewman@stanford.edu — Wed, 11 Nov 2009 10:24:34 -0800

Falconer Biology Library

EndNote Web

mnewman@stanford.edu — Wed, 11 Nov 2009 10:21:15 -0800

EndNote Web, a component of EndNote and ISI Web of Knowledge, is a Web-based version of EndNote.

Falconer Biology Library

EndNote

mnewman@stanford.edu — Wed, 11 Nov 2009 10:20:03 -0800

EndNote software is available in Windows and Mac OS versions. The program can be purchased at the Stanford bookstore or through the EndNote website and an academic discount is available for Stanford students.

Falconer Biology Library

RefWorks

mnewman@stanford.edu — Wed, 11 Nov 2009 10:15:33 -0800

Stanford faculty, staff, and students have access to the Web-based RefWorks program from any computer. New to RefWorks? Start with the RefWorks Quick Start Guide. Complete documentation is available in the RefWorks Online Help. RefWorks video tutorials are also available.

Falconer Biology Library

BIO 104/200 Essential Links

mnewman@stanford.edu — Tue, 10 Nov 2009 16:35:54 -0800

Socrates: Stanford's Online Catalog
The catalog of books, journals, digital books and journals, and other materials in the libraries at Stanford.

Electronic Journals and Newspapers (E-journals Page)
Find e-journals available at Stanford.

BIOSIS
BIOSIS indexes journal articles, meeting abstracts, and some books, book chapters, and patents in life sciences from 1926 to the present.

PubMed
PubMed indexes journal articles in medicine and basic biomedical sciences. Links to NCBI molecular sequence and structure data are included in PubMed records.

Falconer Biology Library

E-book sites

mnewman@stanford.edu — Tue, 10 Nov 2009 13:27:13 -0800

Elsevier ScienceDirect

Google Books

National Academies Press

SCI-TECHnetBASE

SpringerLink

Falconer Biology Library

SearchWorks

mnewman@stanford.edu — Tue, 10 Nov 2009 11:51:06 -0800

SearchWorks is the Stanford University Libraries' next generation search engine. It is designed to make it easier to discover and use the wealth of information resources held at SULAIR, and beyond, by providing a comprehensive place to search and browse for academic information resources. SearchWorks incorporates many of the best features of today's web applications to make searching, browsing & finding fast, easy and powerful.

Falconer Biology Library

BIO 104/200 Textbook and Course Readings

mnewman@stanford.edu — Tue, 10 Nov 2009 11:41:06 -0800

Molecular biology of the cell / Bruce Alberts ... [et al.] ; with problems by John Wilson, Tim Hunt. 5th Edition. New York : Garland Science, c2008.

Course Reserves Catalog

Search the Course Reserves Catalog to locate books, media, e-journals, and print copies of book chapters and journal articles available through the libraries.

Falconer Biology Library

Top Ten Journals

mnewman@stanford.edu — Tue, 10 Nov 2009 11:03:22 -0800

The top ten journals in Biochemistry and Molecular Biology by Impact Factor from ISI Journal Citation Reports.

Cell
Impact Factor (2008)=31.253

Annual Review of Biochemistry
Impact Factor (2008)=30.016

Falconer Biology Library

SciFinder Scholar

mnewman@stanford.edu — Mon, 09 Nov 2009 14:04:56 -0800

SciFinder Scholar is a graphical software package that lets you perform selected types of searches in Chemical Abstracts Online with little or no training. Seaches include author searches, subject searches with "natural language" questions, chemical substances by name, structure (exact or family), formula, and CAS Registry Number, Chemical reactions by specifying one structure of interest, Patent or CA Number to find an abstract, refine results by author name, document type, or publication year Macintosh and Windows versions of SciFinder Scholar are available.

Falconer Biology Library

Dissertations & Theses, A&I

mnewman@stanford.edu — Mon, 09 Nov 2009 13:50:16 -0800

The ProQuest Dissertations & Theses electronic database is the world’s most comprehensive collection of dissertations and theses. It includes over 2.5 million citations to dissertations from thousands of graduate schools around the world.

Falconer Biology Library

Finding journals for BIO 104/200

mnewman@stanford.edu — Mon, 09 Nov 2009 13:34:31 -0800

Falconer Biology Library

Electronic Journals and Newspapers (E-journals Page)

mnewman@stanford.edu — Mon, 09 Nov 2009 13:21:45 -0800

The E-journals List presents a searchable and browsable list of digital journals available to the Stanford community. Clicking on a journal title opens a window that displays all available sources for that title with years of coverage.

Falconer Biology Library

Socrates: Stanford's Online Catalog

mnewman@stanford.edu — Mon, 09 Nov 2009 13:17:32 -0800

Socrates is the catalog of books, journals, digital books, digital journals, maps, dissertations, and other materials in the libraries at Stanford University. Search or browse by keyword, author, title, or subject.

Falconer Biology Library

Journal articles for BIO 104/200

mnewman@stanford.edu — Mon, 09 Nov 2009 10:41:24 -0800

BIOSIS
BIOSIS indexes journal articles, meeting abstracts, and some books, book chapters, and patents in life sciences from 1926 to the present.

Dissertations & Theses, A&I
Dissertations & Theses indexes dissertations submitted at institutions around the world.

PubMed
PubMed indexes journal articles in medicine and basic biomedical sciences. Links to NCBI molecular sequence and structure data are included in PubMed records.

SciFinder scholar

Falconer Biology Library

xSearch

nmayo@stanford.edu — Fri, 16 Oct 2009 13:12:00 -0700

xSearch, developed through the Stanford University Libraries' partnership with Deep Web Technologies, provides Stanford researchers and students with a single search option for multiple online resources. Searches may be limited to specific databases, or all available sources may be searched simultaneously. Search results are merged into one relevance ranked list, and are clustered by topic, author, source publication, publisher, and date. Custom searches using any selection of available databases can be created and re-used.

Falconer Biology Library

SULAIR introduces xSearch

mnewman@stanford.edu — Fri, 16 Oct 2009 12:30:58 -0700

Recently Stanford University Libraries & Academic Information Resources (SULAIR) released xSearch for use by the Stanford community. Developed through a partnership with Deep Web Technologies, xSearch provides Stanford researchers and students with a single search option for multiple online resources.

Falconer Biology Library

xSearch

nmayo@stanford.edu — Fri, 16 Oct 2009 12:23:26 -0700

Falconer Biology Library

Spiders and webs at Falconer Library

mnewman@stanford.edu — Thu, 08 Oct 2009 17:03:15 -0700

To celebrate Halloween, the October display in Falconer Biology Library focuses on books about spiders and webs.

Falconer Biology Library

ResearchGATE Scientific Network

cwelborn@stanford.edu — Thu, 24 Sep 2009 14:38:00 -0700

ResearchGATE is a free professional network for scientists. It promotes communication with other scientists, discovery of new methods, papers, and people through a research based search engine, and collaboration using a suite of applications built specifically for researchers.

Falconer Biology Library

New feature: tutorials and interactive guides

mnewman@stanford.edu — Mon, 14 Sep 2009 16:58:08 -0700

Falconer Biology Library’s home page now includes a link to a page of Tutorials and Interactive Guides . Brief videos created at Falconer demonstrate how to find journals in Socrates, how to find journals using the Ejournals page, and how to use BIOSIS Previews, the index to journal articles in the life sciences.

Falconer Biology Library

National Biological Information Infrastructure

cwelborn@stanford.edu — Tue, 08 Sep 2009 13:18:23 -0700

The National Biological Information Infrastructure (NBII) is a broad, collaborative program to provide increased access to data and information on the nation's biological resources. The NBII links diverse, high-quality biological databases, information products, and analytical tools maintained by NBII partners and other contributors in government agencies, academic institutions, non-government organizations, and private industry.

Falconer Biology Library

Tetrahymena Genome Database (TGD)

cwelborn@stanford.edu — Thu, 20 Aug 2009 15:14:54 -0700

TGD is a web-accessible database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community, and many other sources.

Falconer Biology Library

Stanford Microarray Database

cwelborn@stanford.edu — Thu, 20 Aug 2009 15:11:20 -0700

The Stanford Microarray Database (SMD) is a research tool and archive that allows researchers to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. Registration is required and fees may apply.

Falconer Biology Library

Scirus

cwelborn@stanford.edu — Thu, 20 Aug 2009 14:53:11 -0700

Scirus, developed by Elsevier, is a science-specific Internet search engine, searching over 485 million science-specific Web pages.

Falconer Biology Library

Rat Genome Database

cwelborn@stanford.edu — Thu, 20 Aug 2009 14:28:45 -0700

The Rat Genome Database is a collaborative effort among research institutions involved in rat genetic and genomic research. Its goal is to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.

Falconer Biology Library

Transeq

cwelborn@stanford.edu — Thu, 20 Aug 2009 14:24:34 -0700

Transeq translates nucleic acid sequences to the corresponding peptide sequence. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames.

Falconer Biology Library

PlantGDB

cwelborn@stanford.edu — Thu, 20 Aug 2009 14:18:42 -0700

PlantGDB is an NSF-funded project to develop plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.

Falconer Biology Library

PANTHER Classification System

cwelborn@stanford.edu — Thu, 20 Aug 2009 14:15:36 -0700

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.

Falconer Biology Library

National Brain Databank

cwelborn@stanford.edu — Wed, 19 Aug 2009 16:24:08 -0700

The National Brain Databank was established by the Harvard Brain Tissue Resource Center as a publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders.

Falconer Biology Library

Motif Alignment and Search Tool (MAST)

cwelborn@stanford.edu — Wed, 19 Aug 2009 16:20:21 -0700

MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs.

Falconer Biology Library

miRNAMap

cwelborn@stanford.edu — Wed, 19 Aug 2009 16:18:10 -0700

MicroRNAs (miRNAs) are small noncoding RNA molecules, which are capable of negatively regulating gene expression to control cellular mechanisms. miRNAMap is a database of experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes.

Falconer Biology Library

Mammalian Gene Collection (MGC)

cwelborn@stanford.edu — Wed, 19 Aug 2009 16:16:03 -0700

The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide researchers with unrestricted access to sequence-validated full-length protein-coding (FL-CDS) cDNA clones for human, mouse, and rat genes. In 2005, the project added the cow cDNAs generated by Genome Canada.

Falconer Biology Library

KEGG

cwelborn@stanford.edu — Wed, 19 Aug 2009 16:08:29 -0700

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping.

Falconer Biology Library

International Mouse Strain Resource (IMSR)

cwelborn@stanford.edu — Wed, 19 Aug 2009 16:05:19 -0700

The IMSR, sponsored by the Jackson Laboratory, is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant, and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research.

Falconer Biology Library

Human Protein Atlas

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:58:33 -0700

The human protein atlas shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry images and immunofluorescence confocal microscopy images.

Falconer Biology Library

HOVERGEN

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:48:21 -0700

HOVERGEN is a database of homologous vertebrate genes, structured under the ACNUC sequence database management system. It allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.

Falconer Biology Library

HiMAP

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:40:55 -0700

HiMAP is a dynamic browser for the human protein-protein interaction map. HiMAP allows users to begin with a single protein or a set of proteins and explore both known and predicted protein-protein interactions. Individual registration is required.

Falconer Biology Library

Gramene

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:37:41 -0700

Gramene is a curated, open-source data resource for comparative genome analysis in the grasses.

Falconer Biology Library

GPCRDB

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:27:08 -0700

GPCRDB is the information system for G protein-coupled receptors.

Falconer Biology Library

ECR Browser

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:21:20 -0700

The ECR Browser is a dynamic graphical interface that allows users to visualize and analyze Evolutionary Conserved Regions (ECRs) in genomes of sequenced species.

Falconer Biology Library

Database of Interacting Proteins (DIP)

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:12:33 -0700

The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database are curated manually by expert curators and automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the core subset of the DIP data. Individual registration is required.

Falconer Biology Library

Database for Annotation, Visualization and Integrated Discovery (DAVID)

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:09:53 -0700

DAVID, maintained by the National Institute of Allergy and Infectious Diseases (NIAID), provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind a large list of genes.

Falconer Biology Library

Cytokines & Cells Online Pathfinder Encyclopaedia (COPE)

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:06:07 -0700

Horst Ibelgaufts' COPE is the updated and revised internet version of the "Dictionary of Cytokines" that appeared in print in 1995. This book itself was an updated version of the German "Lexikon Zytokine" published in 1992.

Falconer Biology Library

Comprehensive Microbial Resource (CMR)

cwelborn@stanford.edu — Wed, 19 Aug 2009 15:03:00 -0700

The Comprehensive Microbial Resource (CMR) is a free website used to display information on all of the publicly available, complete prokaryotic genomes. In addition to the convenience of having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes.

Falconer Biology Library

CAMERA, Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis

cwelborn@stanford.edu — Wed, 19 Aug 2009 14:58:49 -0700

The aim of the CAMERA project is to serve the needs of the microbial ecology research community by creating a rich, distinctive data repository and a bioinformatics tools resource that will address many of the unique challenges of metagenomic analysis.

Falconer Biology Library

Cold Spring Harbor Protocols

cwelborn@stanford.edu — Wed, 19 Aug 2009 14:54:34 -0700

Cold Spring Harbor Protocols is an interdisciplinary digital journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods—a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratory’s courses and manuals.

Falconer Biology Library

SWISS-MODEL Repository

cwelborn@stanford.edu — Wed, 19 Aug 2009 14:49:40 -0700

The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

Falconer Biology Library

UniPathway

cwelborn@stanford.edu — Wed, 19 Aug 2009 14:16:30 -0700

UniPathway provides a collection of manually curated metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.

Falconer Biology Library

ENZYME Enzyme Nomenclature Database

cwelborn@stanford.edu — Wed, 19 Aug 2009 14:05:52 -0700

ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

Falconer Biology Library

World-2DPAGE Repository

cwelborn@stanford.edu — Wed, 19 Aug 2009 14:04:22 -0700

World-2DPAGE Repository is a public standards-compliant repository for proteomics image data published in the literature.

Falconer Biology Library

SWISS-2DPAGE

cwelborn@stanford.edu — Wed, 19 Aug 2009 13:38:16 -0700

SWISS-2DPAGE contains data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps. You can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from UniProtKB/Swiss-Prot.

Falconer Biology Library

Prosite

cwelborn@stanford.edu — Wed, 19 Aug 2009 13:31:36 -0700

PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

Falconer Biology Library

BindingDB

cwelborn@stanford.edu — Wed, 19 Aug 2009 13:28:34 -0700

The Binding Database project aims to make experimental data on the noncovalent association of molecules in solution searchable via the WWW. The initial focus is on biomolecular systems, but data on host-guest and supramolecular systems are also important and will be included in time

Falconer Biology Library

Allen Mouse Brain Atlas

cwelborn@stanford.edu — Wed, 19 Aug 2009 13:26:38 -0700

The Allen Mouse Brain Atlas is an interactive, genome-wide image database of gene expression. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Atlases for the developing mouse brain, the mouse spinal cord, and the human cerebral cortex have been added to the original atlas of the adult mouse brain.

Falconer Biology Library

PubMed Central

nmayo@stanford.edu — Mon, 17 Aug 2009 12:43:03 -0700

PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to the full text of articles in PMC is free, except where a journal requires a subscription for access to recent articles.

Falconer Biology Library

PubChem Substance

nmayo@stanford.edu — Mon, 17 Aug 2009 12:41:32 -0700

PubChem Substance contains descriptions of chemical samples, from a variety of public sources, and links to information on their biological activities. The description includes links to PubChem Compound in cases where the chemical structures of compounds in the sample are known. Links providing information on biological activity include links to PubMed citations, protein 3D structures, and to biological screening results available in PubChem BioAssay.

Falconer Biology Library

PubChem Compound

nmayo@stanford.edu — Mon, 17 Aug 2009 12:39:54 -0700

PubChem Compound contains chemical structure information drawn from a variety of public sources. Compounds may be searched by chemical properties and are pre-clustered into identity and similarity groups by structure comparison. Whenever possible, compounds are linked via PubChem Substance to information on their biological activities. Available links include PubMed citations, protein 3D structures and links to biological screening results available in PubChem BioAssay.

Falconer Biology Library

PubChem BioAssay

nmayo@stanford.edu — Mon, 17 Aug 2009 12:09:33 -0700

PubChem BioAssay contains the results of biological activity screening from a variety of public sources. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. PubChem BioAssay results are linked to PubChem Substance, and in turn to PubChem Compound, whenever chemical structures are known. Screening results may be browsed via a web interface and also downloaded for further cheminformatics analysis.

Falconer Biology Library

NCBI Taxonomy

nmayo@stanford.edu — Mon, 17 Aug 2009 12:07:21 -0700

The NCBI Taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.

Falconer Biology Library

Entrez UniSTS

nmayo@stanford.edu — Mon, 17 Aug 2009 11:58:47 -0700

UniSTS is a NCBI resource that reports information about markers, or Sequence Tagged Sites (STS). UniSTS integrates marker and mapping data from public resources including GenBank, RHdb, GDB, various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).

Falconer Biology Library

Entrez UniGene

nmayo@stanford.edu — Mon, 17 Aug 2009 11:56:50 -0700

UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.

Falconer Biology Library

Entrez 3D Domains

nmayo@stanford.edu — Mon, 17 Aug 2009 11:55:01 -0700

3D Domains are compact structural domains identified automatically in MMDB, Entrez's macromolecular three-dimensional structure database. 3D Domains are the units of comparison for structure neighbor calculations using the VAST algorithm. Links to VAST or 3D Domain neighbors display 3D Domains (and complete polypeptide chains) with similar 3D structures.

Falconer Biology Library

Entrez SRA

nmayo@stanford.edu — Mon, 17 Aug 2009 11:53:24 -0700

SRA is a database of raw sequence data from sequencing instruments.

Falconer Biology Library

Entrez SNP

nmayo@stanford.edu — Mon, 17 Aug 2009 11:51:32 -0700

SNP is NCBI’s database of Single Nucleotide Polymorphisms.

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Entrez Protein Clusters

nmayo@stanford.edu — Fri, 14 Aug 2009 15:56:19 -0700

Protein Clusters is a collection of related protein sequences (clusters). Currently it consists of Reference Sequence proteins encoded by complete prokaryotic and chloroplast genomes and plasmids. This database contains both curated and non-curated clusters.

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Entrez Probe

nmayo@stanford.edu — Fri, 14 Aug 2009 15:54:53 -0700

The Probe Database is a public registry of sequence-specific reagents designed for use in a wide variety of biomedical research applications, together with information on reagent availability, experimental protocols, probe effectiveness, and computed sequence similarities.

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Entrez PopSet

nmayo@stanford.edu — Fri, 14 Aug 2009 15:52:17 -0700

PopSet is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. They are submitted to GenBank via Sequin, often as a sequence alignment.

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Entrez Peptidome

nmayo@stanford.edu — Fri, 14 Aug 2009 15:50:19 -0700

Peptidome a repository of tandem mass spectrometry peptide and protein identification data generated by the scientific community.

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Entrez OMIM

nmayo@stanford.edu — Fri, 14 Aug 2009 15:48:43 -0700

Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. It is based on the book, Mendelian Inheritance in Man. The online version is updated daily. The OMIM FAQs provide additional information about the book and the online database.

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Entrez OMIA

nmayo@stanford.edu — Fri, 14 Aug 2009 15:47:09 -0700

Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in animal species (other than human and mouse) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. The database contains textual information and references, as well as links to other relevant records.

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Entrez MeSH

nmayo@stanford.edu — Fri, 14 Aug 2009 15:45:31 -0700

MeSH is NLM's controlled vocabulary used for indexing articles in PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts. Use the MeSH database to build a PubMed search strategy.

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Entrez Journals

nmayo@stanford.edu — Fri, 14 Aug 2009 15:43:48 -0700

The Entrez Journals database searches for a journal and has links to records for that journal in the databases. The Journals database can be searched using the journal title, MEDLINE abbreviation, NLM ID, ISO abbreviation, or ISSN. The database includes the journals in all Entrez databases, e.g., PubMed, Nucleotide, Protein.

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Entrez HomoloGene

nmayo@stanford.edu — Fri, 14 Aug 2009 15:42:01 -0700

HomoloGene is an automated system for detecting homologs among the annotated genes of several completely sequenced eukaryotic genomes.

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Entrez GSS

nmayo@stanford.edu — Fri, 14 Aug 2009 15:40:18 -0700

The GSS database contains all records found within the Genome Survey Sequence (GSS) division of GenBank. GSS records contain first-pass single-read genomic sequences and rarely include annotated biological features.

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Entrez GEO Profiles

nmayo@stanford.edu — Fri, 14 Aug 2009 15:38:12 -0700

Individual gene expression and molecular abundance profiles assembled from the Gene Expression Omnibus (GEO) repository. Entrez GEO Profiles queries annotation and pre-computed profile characteristics, allowing identification of specific genes, and molecular abundance profiles of interest.

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Entrez GEO Profiles

nmayo@stanford.edu — Thu, 13 Aug 2009 16:46:10 -0700

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Entrez GEO DataSets

nmayo@stanford.edu — Thu, 13 Aug 2009 16:42:42 -0700

Comparable experimental sample sets assembled from the Gene Expression Omnibus (GEO) repository. Entrez GDS queries all GEO DataSet annotation, allowing identification of experiments of interest.

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Entrez GENSAT

nmayo@stanford.edu — Thu, 13 Aug 2009 16:40:52 -0700

The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. The GENSAT database contains mouse brain images at several different developmental stages using both techniques, with a searchable set of gene expression annotations.

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Entrez Genome Project

nmayo@stanford.edu — Thu, 13 Aug 2009 16:38:42 -0700

Genome Project is a collection of complete and incomplete large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved.

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Entrez Gene

nmayo@stanford.edu — Thu, 13 Aug 2009 16:36:24 -0700

Gene organizes information about the characteristics and defining sequences of genes from species in Genome, RefSeq, and other model organisms.

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Entrez EST

nmayo@stanford.edu — Thu, 13 Aug 2009 16:34:09 -0700

The EST database contains all records found within the Expressed Sequence Tag (EST) division of GenBank. EST records contain first-pass single-read cDNA sequences and include no annotated biological features.

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Entrez dbGaP

nmayo@stanford.edu — Wed, 12 Aug 2009 15:58:07 -0700

The database of genotype and phenotype (dbGaP) stores phenotype and genotype data, as well as the associations between them. Studies generating data for dbGaP will include genome-wide association studies, medical sequencing, and molecular diagnostic assays. Summaries of phenotype and genotype data as well as study documents and association analyses (when available) will be found on the public site. Authorized access may be required for downloading coded individual-level phenotypes genotypes and pedigrees.

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Entrez CDD

nmayo@stanford.edu — Wed, 12 Aug 2009 15:56:28 -0700

CDD currently contains domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI, such as COG. The source databases also provide descriptions and links to citations. Since conserved domains correspond to compact structural units, CDs contain links to 3D-structure via Cn3D whenever possible.

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Entrez Cancer Chromosomes

nmayo@stanford.edu — Wed, 12 Aug 2009 15:54:05 -0700

Cancer Chromosomes contains three cancer cytogenetic databases: the NCI Mitelman Database of Chromosome Aberrations in Cancer, the NCI Recurrent Chromosome Aberrations in Cancer, and the NCI and NCBI SKY/M-FISH & CGH Database. Karyotype, SKY/M-FISH, and CGH data can be searched simultaneously. Similarity searches demonstrate cytogenetic and clinical relatedness at varying levels of specificity.

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Entrez Books

nmayo@stanford.edu — Wed, 12 Aug 2009 15:40:13 -0700

In collaboration with authors and publishers, the National Center for Biotechnology Information (NCBI) is adapting biomedical Books for the web.

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Protein Analysis NCBI Entrez

nmayo@stanford.edu — Wed, 12 Aug 2009 13:56:27 -0700

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Nucleic Acid NCBI Entrez

nmayo@stanford.edu — Wed, 12 Aug 2009 13:53:08 -0700

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Genetics and Genomics NCBI Entrez

nmayo@stanford.edu — Wed, 12 Aug 2009 13:46:18 -0700

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Cell Biology NCBI Entrez

nmayo@stanford.edu — Wed, 12 Aug 2009 13:34:48 -0700

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Experimental Factor Ontology (EFO)

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:33:10 -0700

The Experimental Factor Ontology (EFO) is an application focused ontology modeling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data.

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EMBL Nucleotide Sequence Database

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:27:36 -0700

The EMBL Nucleotide Sequence Database (also known as EMBL-Bank), maintained by EMBL-EBI, is Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis.

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EGA, European Genome-phenome Archive

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:25:51 -0700

The European Genome-phenome Archive (EGA), maintained by EMBL-EBI, is designed to be a repository for all types of genotype experiments, including case control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. This data may be either publicly available or limited access, depending on the design of the study.

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DSSP

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:23:59 -0700

The DSSP program was designed to standardize secondary structure assignment. The DSSP database is a database of secondary structure assignments (and much more) for all of the entries in the Protein Data Bank (PDB).

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CSA, Catalytic Site Atlas

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:21:52 -0700

The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. The classification of catalytic residues includes only those residues thought to be directly involved in some aspect of the reaction catalyzed by an enzyme.

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CluSTr

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:20:15 -0700

The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences.

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CiteXplore

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:17:29 -0700

CiteXplore combines literature searches of MEDLINE/PubMed and full-text databases such as PubMedCentral and patents with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available.

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ChEBI

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:15:28 -0700

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

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BioModels Database: a Database of Annotated Published Models

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:13:28 -0700

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.

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ATSD, Alternative Spicing and Transcript Diversity

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:11:33 -0700

The Alternative Splicing and Transcript Diversity (ASTD) database project, maintained by EMBL-EBI, is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale.

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ArrayExpress

cwelborn@stanford.edu — Fri, 31 Jul 2009 15:10:07 -0700

ArrayExpress is a public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with MGED recommendations. The Gene Expression Atlas uses a curated, re-annotated subset of data from the Archive to provide information about gene expression under various biological conditions.

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Entrez BioSystems

cwelborn@stanford.edu — Fri, 31 Jul 2009 14:57:50 -0700

The BioSystems database contains records that group together molecules that interact in biological systems. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs.

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Institute of Human Origins (IHO)

kistuart@stanford.edu — Mon, 20 Jul 2009 11:28:08 -0700

Directed by Donald C. Johanson, the scientific mission of IHO is the strategic implementation of multidisciplinary field and laboratory research on the fossil evidence for human evolution.

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Museum of Comparative Zoology

kistuart@stanford.edu — Mon, 20 Jul 2009 11:26:39 -0700

The Museum of Comparative Zoology (MCZ) at Harvard University is a center for research and education focused on the comparative relationships of animal life. The present-day MCZ collections are comprised of approximately 21-million extant and fossil invertebrate and vertebrate specimens, which continue to be a focus of research and teaching for MCZ, Harvard and outside students and researchers.

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MacClade

kistuart@stanford.edu — Mon, 20 Jul 2009 11:25:16 -0700

MacClade is a computer program for phylogenetic analysis written by David Maddison and Wayne Maddison. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.

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LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence

kistuart@stanford.edu — Mon, 20 Jul 2009 11:24:01 -0700

LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates.

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TreeView

kistuart@stanford.edu — Mon, 20 Jul 2009 11:23:09 -0700

Tree drawing software for Apple Macintosh and Windows.

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Alfred Russel Wallace Page

kistuart@stanford.edu — Mon, 20 Jul 2009 11:21:36 -0700

This provides a summary of evolutionist Alfred Russel Wallace’s accomplishments and a record of his writings in the hope that his contributions to knowledge might become better recognized and provoke more of the kind of fearless and impassioned reasoning he was famous for.

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Phylogeny Programs

kistuart@stanford.edu — Mon, 20 Jul 2009 11:20:13 -0700

For advanced students of evolution, this site contains a comprehensive list of all known phylogenetics software. It is compiled and updated bi-annually by Joe Felsenstein, creator of PHYLIP phylogenetic inference software, at the University of Washington.

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NESCent National Evolutionary Synthesis Center

kistuart@stanford.edu — Mon, 20 Jul 2009 11:19:16 -0700

NESCent, The National Evolutionary Synthesis Center, is a collaborative effort of Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University and is sponsored by the National Science Foundation. Its mission is to facilitate broadly synthetic research to address fundamental questions in evolutionary biology.

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Issues in Evolution (Action Bioscience)

kistuart@stanford.edu — Mon, 20 Jul 2009 11:18:16 -0700

ActionBioscience.org is a non-commercial, educational web site created to promote bioscience literacy by examining issues, and has compiled a collection of scholarly articles on evolution.

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Becoming Human

kistuart@stanford.edu — Mon, 20 Jul 2009 11:16:50 -0700

Becoming Human brings together interactive multimedia, research and scholarship to promote greater understanding of the course of human evolution.

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PHYLIP: Phylogenetic Inference Software

kistuart@stanford.edu — Mon, 20 Jul 2009 11:15:53 -0700

This site allows users to download PHYLIP, a free software package that infers evolutionary relationships between taxa using one of a variety of inference methods. PHYLIP is available in several formats and is recommended for advanced students of evolution.

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PBS Evolution

kistuart@stanford.edu — Mon, 20 Jul 2009 11:14:35 -0700

The PBS Evolution Web site is intended to serve as a comprehensive learning resource about evolutionary science for teachers, students and the general public. There are seven main topic, along with a searchable multimedia library containing graphics, websites, journals, programs, lessons, and print material.

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Encyclopedia of Evolution

kistuart@stanford.edu — Mon, 20 Jul 2009 10:00:01 -0700

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Encyclopedia of Entomology

kistuart@stanford.edu — Mon, 20 Jul 2009 09:59:05 -0700

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University of California Museum of Paleontology

kistuart@stanford.edu — Mon, 20 Jul 2009 09:56:51 -0700

The University of California Museum of Paleontology presents its exhibits, collections, time lines, research, and more in this comprehensive site. "Understanding Evolution" is its popular learning tool, which teaches the fundamental concepts of evolution, such as its impact, evidence, and theory.

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Tree of Life Web Project

kistuart@stanford.edu — Mon, 20 Jul 2009 09:55:21 -0700

The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny).

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Society for the Study of Evolution

kistuart@stanford.edu — Mon, 20 Jul 2009 09:47:39 -0700

The website for the Society for the Study of Evolution promotes the study of organic evolution with links to its journal Evolution and updates on its news and meetings.

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Evolution Research News

kistuart@stanford.edu — Mon, 20 Jul 2009 09:46:04 -0700

This “academic guide to evolution news and research” contains an extensive list of newspapers, journals, books, websites, and other Internet resources on the topic of evolution.

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Complete Work of Charles Darwin Online

kistuart@stanford.edu — Mon, 20 Jul 2009 09:43:11 -0700

The most extensive online collection of Charles Darwin’s published and unpublished papers is offered on this site, with much of it available as searchable text.

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Animal Behavior Desk Reference: A Dictionary of Animal Behavior, Ecology, and Evolution

kistuart@stanford.edu — Mon, 20 Jul 2009 09:40:26 -0700

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Early Human Phylogeny

kistuart@stanford.edu — Mon, 20 Jul 2009 09:33:01 -0700

This is the Smithsonian National Museum of Natural History’s interactive human phylogenetic tree. Pictures of fossil remains and descriptors of hominids are linked.

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UniProt

kistuart@stanford.edu — Sat, 18 Jul 2009 22:26:23 -0700

The Universal Protein Resource (UniProt), maintained by EMBL-EBI, is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.

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Systems Biology Ontology (SBO)

kistuart@stanford.edu — Sat, 18 Jul 2009 22:25:18 -0700

SBO is the Systems Biology Ontologies project, another cornerstone of the BioModels.net effort. The goal of SBO is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling.

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Similarity and Homology

kistuart@stanford.edu — Sat, 18 Jul 2009 22:24:19 -0700

This page, maintained by the European Bioinformatics Institute, lists various sequence database similarity search tools such as FASTA, BLAST, MPsrch and ScanPS. Interactive as well as email submissions are available for each of these services.

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Rhea

kistuart@stanford.edu — Sat, 18 Jul 2009 22:23:10 -0700

Rhea is a freely available, manually annotated database of chemical reactions created by EMBL-EBI in collaboration with the Swiss Institute of Bioinformatics (SIB).

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RESID Database at the EBI

kistuart@stanford.edu — Sat, 18 Jul 2009 22:18:55 -0700

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

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RADAR

kistuart@stanford.edu — Sat, 18 Jul 2009 22:17:46 -0700

RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. Radar is uses an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence.

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ProFunc

kistuart@stanford.edu — Sat, 18 Jul 2009 22:16:45 -0700

The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods to try to provide clues as the the protein's likely or possible function.

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Pratt Pattern Matching

kistuart@stanford.edu — Sat, 18 Jul 2009 22:15:35 -0700

An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to search for patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.

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PPSearch

kistuart@stanford.edu — Sat, 18 Jul 2009 22:14:24 -0700

This tool allows you to search your query sequence for protein motifs. You can rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database.

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Phobius

kistuart@stanford.edu — Sat, 18 Jul 2009 22:11:42 -0700

The Phobius server is for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.

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PDBsum

kistuart@stanford.edu — Sat, 18 Jul 2009 22:10:04 -0700

PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

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PDBe

kistuart@stanford.edu — Sat, 18 Jul 2009 22:09:05 -0700

The Protein Structure Database in Europe (PDBe), maintained by EMBL-EBI, is a project for the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB).

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Parasite Genome Databases and Genome Research Resources

kistuart@stanford.edu — Sat, 18 Jul 2009 22:08:08 -0700

This page, maintained by EMBL-EBI, lists resources for research on parasite genomes.

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NEWT

kistuart@stanford.edu — Sat, 18 Jul 2009 22:06:55 -0700

NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data compiled in the NCBI database and data specific to the UniProt Knowledgebase.

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MSDchem

kistuart@stanford.edu — Sat, 18 Jul 2009 22:05:21 -0700

MSDchem is a consistent and enriched library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry.

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MaxSprout

kistuart@stanford.edu — Sat, 18 Jul 2009 22:03:00 -0700

MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimised in rotamer space using a rough potential energy function to avoid clashes.

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LGIC, Ligand-Gated Ion Channel Database

kistuart@stanford.edu — Sat, 18 Jul 2009 22:00:51 -0700

In the LGIC Database you will find the nucleic acid and protein sequences of ligand-gated ion channel subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.

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Karyn’s Genomes

kistuart@stanford.edu — Sat, 18 Jul 2009 21:59:28 -0700

Karyn’s Genomes, maintained by EMBL-EBI, is a collection and brief description of some of the available sequenced genomes. There is also information about why they are thought to be important for sequencing, together with links to the sequences, publication data and further reading.

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IPI, International Protein Index

kistuart@stanford.edu — Sat, 18 Jul 2009 21:57:20 -0700

IPI, maintained by EMBL-EBI, provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms.

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IPD, Immuno Polymorphism Database

kistuart@stanford.edu — Sat, 18 Jul 2009 21:52:23 -0700

The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. The IPD project was established by the HLA Informatics Group of the Anthony Nolan Research Institute in close collaboration with the European Bioinformatics Institute.

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InterProScan Sequence Search

kistuart@stanford.edu — Sat, 18 Jul 2009 21:50:51 -0700

InterProScan Sequence Search allows you to query your sequence against InterPro.

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InterPro

kistuart@stanford.edu — Sat, 18 Jul 2009 21:49:48 -0700

InterPro, maintained by EMBL-EBI, is a database of protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.

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IntEnz

kistuart@stanford.edu — Sat, 18 Jul 2009 21:48:42 -0700

IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created by EMBL-EBI in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

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Integr8, Access to Complete Genomes and Protomes

kistuart@stanford.edu — Sat, 18 Jul 2009 21:33:33 -0700

The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.

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IntAct

kistuart@stanford.edu — Sat, 18 Jul 2009 21:32:22 -0700

IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions.

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IMGT/HLA

kistuart@stanford.edu — Sat, 18 Jul 2009 21:30:59 -0700

IMGT, the international ImMunoGeneTics information system, is an integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species.

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Human Proteome Initiative (HPI)

kistuart@stanford.edu — Sat, 18 Jul 2009 21:28:28 -0700

The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences and their mammalian orthologs, according to the quality standards of UniProtKB/Swiss-Prot.

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HUGO Gene Nomenclature Committee

kistuart@stanford.edu — Sat, 18 Jul 2009 21:27:10 -0700

HGNC is a web site hosted at the European Bioinformatics Institute. It aims to assign a unique approved gene symbol and name to every gene in the human genome. Standardized gene nomenclature is now widely recognized as an invaluable resource for all researchers and is prominently listed in numerous databases such as Ensembl, Entrez Gene, GeneCards, the UCSC Genome Browser and UniProt.

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Genome Reviews

kistuart@stanford.edu — Sat, 18 Jul 2009 21:25:21 -0700

The Genome Reviews database, maintained by EMBL-EBI, provides an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database.

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Genome Pages

kistuart@stanford.edu — Sat, 18 Jul 2009 21:24:03 -0700

The first completed genomes from viruses, phages and organelles were deposited into the EMBL Database in the early 1980's. Since then, molecular biology's shift to obtain the complete sequences of as many genomes as possible combined with major developments in sequencing technology resulted in hundreds of complete genome sequences being added to the database, including Archaea, Bacteria and Eukaryota. These web pages give access to a large number of complete genomes.

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Gene Ontology Annotation (GOA) Database

kistuart@stanford.edu — Sat, 18 Jul 2009 21:22:27 -0700

The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI) and is a central dataset for other major multi-species databases; such as Ensembl and NCBI.

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Gene Ontology (GO)

kistuart@stanford.edu — Sat, 18 Jul 2009 21:20:21 -0700

The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.

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Gene Expression Atlas

kistuart@stanford.edu — Sat, 18 Jul 2009 21:08:39 -0700

The Gene Expression Atlas (ArrayExpress Atlas), maintained by EMBL-EBI, is a semantically enriched database of meta-analysis based summary statistics which serves queries for condition-specific gene expression patterns (e.g. genes over-expressed in a particular tissue or disease state) as well as broader exploratory searches for biologically interesting genes/samples. It is based on a subset of the ArrayExpress data.

Falconer Biology Library

FSSP (Families of Structurally Similar Proteins)

kistuart@stanford.edu — Sat, 18 Jul 2009 21:00:58 -0700

FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB) [1]. The database currently contains an extended structural family for each of 330 representative protein chains.

Falconer Biology Library

FingerPRINTScan

kistuart@stanford.edu — Sat, 18 Jul 2009 20:59:38 -0700

FingerPRINTScan classifies sequences using familial definitions from the PRINTS database, allowing progress to be made with the identification of distant evolutionary relationships. The approach makes use of the contextual information inherent in a multiple-motif method, and has the power to identify hitherto unidentified relationships in mass genome data.

Falconer Biology Library

Experimental Factor Ontology (EFO)

kistuart@stanford.edu — Sat, 18 Jul 2009 20:56:53 -0700

Falconer Biology Library

Ensembl Genome Browser

kistuart@stanford.edu — Fri, 17 Jul 2009 17:16:59 -0700

Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. It is a comprehensive source of stable annotation with confirmed gene predictions that have been integrated from external data sources. Ensembl annotates known genes and predicts new ones, with functional annotation from InterPro, OMIM, SAGE and gene families.

Falconer Biology Library

EMBL-CDS

kistuart@stanford.edu — Fri, 17 Jul 2009 17:15:39 -0700

EMBL-CDS is a database of nucleotide sequences of the CDS (coding sequence) features, as annotated in EMBL database. EMBL-CDS record contains the nucleotide sequence of the CDS region, accompanying annotation from the parent nucleotide entry and the additional automatically generated annotation.

Falconer Biology Library

EMBL Nucleotide Sequence Database

kistuart@stanford.edu — Fri, 17 Jul 2009 17:13:43 -0700

Falconer Biology Library

EGA, European Genome-phenome Archive

kistuart@stanford.edu — Fri, 17 Jul 2009 17:09:06 -0700

Falconer Biology Library

DSSP

kistuart@stanford.edu — Fri, 17 Jul 2009 17:06:05 -0700

Falconer Biology Library

CSA, Catalytic Site Atlas

kistuart@stanford.edu — Fri, 17 Jul 2009 17:02:47 -0700

Falconer Biology Library

CluSTr

kistuart@stanford.edu — Fri, 17 Jul 2009 17:00:46 -0700

Falconer Biology Library

CiteXplore

kistuart@stanford.edu — Fri, 17 Jul 2009 16:57:10 -0700

Falconer Biology Library

Evolutionary Biology Encyclopedias

kistuart@stanford.edu — Fri, 17 Jul 2009 14:10:52 -0700

Falconer Biology Library

Evolutionary Biology Research Guide

kistuart@stanford.edu — Fri, 17 Jul 2009 13:55:27 -0700

Falconer Biology Library research guide for evolutionary biology

Falconer Biology Library

Evolutionary Biology Web Resources

kistuart@stanford.edu — Fri, 17 Jul 2009 13:40:07 -0700

Falconer Biology Library

ChEBI

kistuart@stanford.edu — Fri, 17 Jul 2009 13:06:15 -0700

Falconer Biology Library

BioModels Database: a Database of Annotated Published Models

kistuart@stanford.edu — Fri, 17 Jul 2009 13:04:07 -0700

Falconer Biology Library

ATSD, Alternative Spicing and Transcript Diversity

kistuart@stanford.edu — Fri, 17 Jul 2009 12:57:36 -0700

Falconer Biology Library

Evolutionary Biology Databases

kistuart@stanford.edu — Fri, 17 Jul 2009 10:27:10 -0700

Falconer Biology Library

ArrayExpress

nmayo@stanford.edu — Fri, 17 Jul 2009 09:33:12 -0700

Falconer Biology Library

Table with images on Evolutionary Biology Research Guide

kistuart@stanford.edu — Thu, 16 Jul 2009 13:35:27 -0700

Use Socrates to find printed or digital books or journals at Stanford. Digital Journals available to the Stanford community are listed in Electronic Journals and Newspapers.

Falconer Biology Library

OneFish Community Directory

cwelborn@stanford.edu — Tue, 14 Jul 2009 09:14:52 -0700

With an overall focus on fisheries research and development, the OneFish Community Directory comprises an open-access, interactive internet portal in which knowledge of many types is referenced, linked to or uploaded, including news, events, jobs, documents, projects, websites and multimedia. Online discussions are either archived or hosted in OneFish and polls can be initiated. Knowledge is added manually by members and editors, or `captured' electronically from originators' systems.

Falconer Biology Library

Falconer Biology Library launches its new website

mnewman@stanford.edu — Thu, 09 Jul 2009 16:22:02 -0700

On July 1, 2009, Falconer Biology Library completed the final step in launching its new website by deleting links to the old site and redirecting old URLs to the new site. The process of planning, design, and development of the new site has taken nearly a year, and this work is a part of a larger effort to enhance and update websites across the science and engineering libraries at Stanford.

Falconer Biology Library

Tutorials & Interactive Guides

kistuart@stanford.edu — Mon, 06 Jul 2009 12:24:38 -0700

These interactive guides and tutorials will help you use key resources for biology.

EndNote

Falconer Biology Library

Access to LANL databases will be discontinued

mnewman@stanford.edu — Tue, 30 Jun 2009 12:43:58 -0700

After August 31, 2009, OPPIE, LANL’s database search system, will no longer be available to Stanford users. The subscription to OPPIE will be discontinued because all databases offered through LANL’s system are now available at Stanford through other platforms, primarily Web of Science/Web of Knowledge. In addition, Los Alamos National Laboratory plans to cease offering the OPPIE system in the near future.

Falconer Biology Library

OskiCat replaces Pathfinder at UC Berkeley

mnewman@stanford.edu — Thu, 25 Jun 2009 14:27:34 -0700

On June 24, 2009, OskiCat replaced Pathfinder and GLADIS as the UC Berkeley library catalog. If you’ve used Pathfinder, OskiCat will look familiar but with OskiCat you can:

Find books and journals from more UCB campus libraries, including the Institutes of Governmental Studies and Transportation Studies Libraries and the Water Resources Center Archives.
Limit results to available items.
- Falconer Biology Library
read more

SearchWorks (prototype)

nmayo@stanford.edu — Fri, 15 May 2009 16:31:49 -0700

Mathematical and Computer Sciences Library

Google Books

nmayo@stanford.edu — Tue, 28 Apr 2009 14:01:48 -0700

Falconer Biology Library

E-Book Resources

nmayo@stanford.edu — Tue, 28 Apr 2009 11:37:33 -0700

Following is a list of selected electronic book resources that have material related to the Life Sciences. Many individual titles can be found in the Stanford library catalog, Socrates, where you can limit your search to online resources by clicking on the "Electronic Resources" tab on the Search page.

AccessScience
The online McGraw Hill Encyclopedia of Science and Technology. A collection of articles, bibliographies, study guides, dictionaries, etc.

ebrary

Falconer Biology Library

Fungal Genetics Stock Center

nmayo@stanford.edu — Thu, 23 Apr 2009 12:18:10 -0700

The Fungal Genetics Stock Center at the University of Missouri preserves strains of fungi that are used in genetics research. Currently the center preserves over 10,000 strains of /Neurospora/ in addition to strains of /Aspergillus/ and representatives of other taxa. The center’s website provides information for researchers who are interested in ordering strains and presents links to resources on /Neurospora, Aspergillus/, and other fungi.

Falconer Biology Library

Library Catalog (SOCRATES)

nmayo@stanford.edu — Fri, 20 Mar 2009 16:16:47 -0700

Mathematical and Computer Sciences Library

E-Journals

nmayo@stanford.edu — Thu, 19 Mar 2009 16:58:32 -0700

Mathematical and Computer Sciences Library

Department of Global Ecology, Carnegie Institution for Science

nmayo@stanford.edu — Thu, 19 Mar 2009 09:13:00 -0700

The Department of Global Ecology, founded in 2002 on the campus of Stanford University, conducts basic research on the interactions among the earth's ecosystems, land, atmosphere, and oceans. The goal of this research is to understand the ways in which these interactions shape the behavior of the earth system, including its responses to future changes. The department’s website presents news from the department, a list of personnel, descriptions of current research, and a list of the department’s publications and theses.

Falconer Biology Library

SpringerLink offers print-on-demand books through MyCopy

mnewman@stanford.edu — Tue, 03 Mar 2009 10:30:50 -0800

The libraries at Stanford are purchasing increasing numbers of digital books and these ebooks are becoming easier to find in Socrates, the library catalog.

Falconer Biology Library

Charles Darwin, Alfred Russel Wallace, and Evolution

mnewman@stanford.edu — Fri, 27 Feb 2009 15:51:37 -0800

Falconer Biology Library’s monthly display for March celebrates the life and work of Charles Darwin on the two hundredth anniversary of his birth in Shrewsbury, Shropshire. On display are books by and about Darwin and evolutionary theory.

Falconer Biology Library

Website feedback

cwelborn@stanford.edu — Tue, 24 Feb 2009 10:38:37 -0800

We are testing our new website and we need your feedback.

Falconer Biology Library

Biodiversity Heritage Library

nmayo@stanford.edu — Wed, 18 Feb 2009 10:56:26 -0800

Ten major natural history museum libraries, botanical libraries, and research institutions In the United States and the United Kingdom have joined to form the Biodiversity Heritage Library Project. The participating libraries own over two million volumes of biodiversity literature collected over 200 years to support the work of scientists, researchers, and students in their home institutions and throughout the world. The Biodiversity Heritage Library’s “biodiversity commons” website provides digitized access to a growing subset of this literature.

Falconer Biology Library

Complete the Science Libraries User Survey

mnewman@stanford.edu — Tue, 10 Feb 2009 09:18:49 -0800

Through February 17, 2009, the Science and Engineering Libraries at Stanford are conducting a user needs assessment survey. Most people can complete the form in 15 minutes. Find the survey at:

http://tinyurl.com/scilib-survey

Falconer Biology Library

Handbook of Plant Biotechnology

nmayo@stanford.edu — Thu, 05 Feb 2009 16:34:45 -0800

Falconer Biology Library

Encyclopedic Dictionary of Genetics, Genomics, and Proteomics

nmayo@stanford.edu — Thu, 29 Jan 2009 12:54:53 -0800

Falconer Biology Library

Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics

nmayo@stanford.edu — Thu, 29 Jan 2009 12:44:23 -0800

Falconer Biology Library

Encyclopedia of Biostatistics

nmayo@stanford.edu — Thu, 29 Jan 2009 12:38:46 -0800

Falconer Biology Library

CAB Abstracts via ISI Web of Knowledge

mnewman@stanford.edu — Mon, 26 Jan 2009 13:02:42 -0800

CAB Abstracts , the database of journal article citations on agricultural science, veterinary medicine, nutrition, and natural resources, is now available in Web of Knowledge. It joins a collection of useful databases for life scientists: BIOSIS, Web of Science, and Zoological Record. In ISI Web of Knowledge, these databases can be searched simultaneously or separately.

Falconer Biology Library

Wetlands, Oceans, and Watersheds

nmayo@stanford.edu — Tue, 20 Jan 2009 08:56:50 -0800

The Office of Wetlands, Oceans, and Watersheds (OWOW) of the United States Environmental Protection Agency offers information related to protection of wetlands and watersheds. The website includes news and updates from OWOW, information on funding and training opportunities, laws and regulations related to wetlands, EPA databases, watershed and wetland mapping resources, and water quality models. The site also offers quick links to information on topics of interest, including climate change, the National Estuary Program, Gulf of Mexico hypoxia, and water quality trading.

Falconer Biology Library

Monthly display in Falconer Biology Library

mnewman@stanford.edu — Tue, 13 Jan 2009 15:37:56 -0800

Visit Falconer Biology Library in January to view our display, “Diversity: Evolution, Cooperation, Sex, and Gender”.

Falconer Biology Library

Highwire Press

nmayo@stanford.edu — Thu, 18 Dec 2008 15:42:41 -0800

Falconer Biology Library

BIOSIS

nmayo@stanford.edu — Fri, 12 Dec 2008 10:28:54 -0800

Also known as BIOSIS Previews, indexes the worldwide literature of research in the biological and biomedical sciences. The database covers the entire field of life sciences including original research reports and reviews in field, laboratory, clinical, experimental, and theoretical work. BIOSIS indexes journals, technical reports, meeting proceedings, United States patents, and books in biology, biomedicine, and related areas. The database indexes literature published from 1926 to the present.

Falconer Biology Library

MaNIS, Mammal Networked Information System

nmayo@stanford.edu — Tue, 09 Dec 2008 09:37:42 -0800

MaNIS, whose development was supported by the National Science Foundation, is a database of records of mammalian specimens held in museums and other institutions in North America. The database can be searched through one of the system’s data portals, and collections can be searched individually or as a group.

Falconer Biology Library

ProPhylER

nmayo@stanford.edu — Thu, 04 Dec 2008 10:20:29 -0800

ProPhylER (Protein Phylogeny and Evolutionary Rates) quantifies evolutionary constraint to annotate functionally or structurally important regions in proteins and to predict the impact of coding polymorphisms. ProPhylER gives the researcher comprehensive constraint data on tens of thousands of eukaryotic proteins, represented by hundreds of thousands of individual sequences.

Falconer Biology Library

Stanford Libraries

nmayo@stanford.edu — Tue, 02 Dec 2008 10:20:35 -0800

Mathematical and Computer Sciences Library

Stanford Home Page

nmayo@stanford.edu — Tue, 02 Dec 2008 10:17:47 -0800

Mathematical and Computer Sciences Library

Journals in the Life Sciences

nmayo@stanford.edu — Fri, 14 Nov 2008 10:56:32 -0800

JOURNALS IN THE LIFE SCIENCES

Journals in the Life Sciences are available in several formats and locations at Stanford University. Check Electronic Journals and Newspapers (E-Journals) for digital format; Socrates for any format, including those not currently received and holdings at Lane Medical Library.

Falconer Biology Library

Encyclopedia of Life Sciences

nmayo@stanford.edu — Thu, 13 Nov 2008 11:49:50 -0800

Falconer Biology Library

Wetlands Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:43:08 -0800

Falconer Biology Library

Sleep Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:39:50 -0800

Falconer Biology Library

Protein Analysis Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:37:20 -0800

Falconer Biology Library

Population Biology Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:34:56 -0800

Falconer Biology Library

Nucleic Acid Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:29:06 -0800

Falconer Biology Library

Insect Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:23:16 -0800

Falconer Biology Library

Genetics and Genomics Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:20:47 -0800

Falconer Biology Library

General Biology Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:18:15 -0800

Falconer Biology Library

Ecology Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:16:11 -0800

Falconer Biology Library

Developmental Biology Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:05:49 -0800

Falconer Biology Library

Cell Biology Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 11:03:01 -0800

Falconer Biology Library

Biodiversity Encyclopedias

nmayo@stanford.edu — Thu, 13 Nov 2008 10:20:59 -0800

Falconer Biology Library

Zoological Record

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:46:19 -0800

Zoological Record indexes the world's zoological and animal science literature, covering all research from biochemistry to veterinary medicine. The database provides a collection of references from over 4,500 international serial publications, plus books, meetings, reviews and other no- serial literature from over 100 countries. It is the oldest continuing database of animal biology, indexing literature published from 1864 to the present. Zoological Record has long been recognized as the "unofficial register" for taxonomy and systematics, but other topics in animal biology are also covered

Falconer Biology Library

Web of Science

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:39:05 -0800

The Web of Science service, available via ISI Web of Knowledge, includes three core component databases: the expanded version of Science Citation Index (SciSearch), Social Sciences Citation Index, and Arts & Humanities Citation Index. The Science Citation Index provides access to current and retrospective bibliographic information, author abstracts, and cited references found in the world's leading scholarly science and technical journals covering over 100 disciplines from 1900 to the present.

Falconer Biology Library

POPLINE

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:34:53 -0800

POPLINE (POPulation information onLINE) contains citations with abstracts to scientific articles, reports, books, and unpublished reports in the field of reproductive health, population, family planning, and related health issues. POPLINE is maintained by the INFO Project at the Johns Hopkins Bloomberg School of Public Health/Center for Communication Programs and is funded by the United States Agency for International Development. (USAID). POPLINE contains nearly 360,000 records.

Falconer Biology Library

PubMed

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:24:15 -0800

Developed by the National Center for Biotechnology Information (NCBI), Pubmed is a free version of MEDLINE that offers links to GenBank records, other molecular sequence data, and other resources. MEDLINE, produced by the National Library of Medicine, is an index to journal articles in medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences, including both basic biomedical sciences and clinical practice. It indexes over 4,000 journals. The database contains citations from 1950 to the present with some older citations.

Falconer Biology Library

Industrial & Applied Microbiology Abstracts (Microbiology A)

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:19:02 -0800

Industrial & Applied Microbiology Abstracts (Microbiology A) indexes journal articles that report significant findings and practical applications in agricultural, food and beverage, chemical, and pharmaceutical industries. Over 360 journals are indexed and the database indexes literature published from 1982 to the present. Specific topics include antibiotic and antimicrobial agents; contamination; ripening and fermentation processes for foods, wines and beer; soil microbiology; plant diseases; biodegradation; and isolation and identification of microorganisms.

Falconer Biology Library

Oceanic Abstracts

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:14:22 -0800

Oceanic Abstracts indexes the worldwide technical literature pertaining to the marine and brackish-water environment. Over 600 journals are indexed and literature published from 1981 to the present is covered. The database focuses on marine biology and physical oceanography, fisheries, aquaculture, non-living resources, meteorology and geology, plus environmental, technological, and legislative topics. It covers living and non-living resources, meteorology and geology, plus environmental, technological, and legislative topics.

Falconer Biology Library

Pollution Abstracts

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:09:17 -0800

Pollution Abstracts indexes material from conference proceedings and hard-to-find documents, in addition to journal articles. Over 1,000 journals are indexed and literature published from 1981 to the present is covered. Topics in pollution and its management are extensively covered from the standpoints of atmosphere, emissions, mathematical models, effects on people and animals, and environmental action.

Falconer Biology Library

Global Population Dynamics Database

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:05:52 -0800

The Global Population Dynamics Database is the largest collection of animal and plant population data in the world, bringing together nearly five thousand time series in one database. Sources of data vary enormously, from annual counts of mammals or birds at individual sampling sites, to weekly counts of zooplankton and other marine fauna.

Falconer Biology Library

Environmental Engineering Abstracts

cwelborn@stanford.edu — Tue, 11 Nov 2008 11:03:41 -0800

Environmental Engineering Abstracts covers the world literature pertaining to technological and engineering aspects of air and water quality, environmental safety, and energy production. Updated monthly, it includes more than 700 indexed primary journals and 2,500 relevant monographs and conference proceedings.

Falconer Biology Library

Environmental Sciences and Pollution Management

cwelborn@stanford.edu — Tue, 11 Nov 2008 10:58:49 -0800

Environmental Sciences and Pollution Management. This database collection, produced by CSA, has 13 subfiles that can be searched individually or as a single database. It offers abstracts for the worldwide literature covering the environmental sciences, including air, land, water and noise pollution, bacteriology, ecology, toxicology, risk assessment, environmental biotechnology and engineering, waste management, water resources, policies and regulations, and U.S. federal environmental impact statements.

Falconer Biology Library

Environmental Fate Database

cwelborn@stanford.edu — Tue, 11 Nov 2008 10:55:15 -0800

Environmental Fate Database, also known as Environmental Issues and Policy Index, provides access to the following databases: DATALOG, which contains 18 types of environmental fate data; BIOLOG, or the Microbial degradation/toxicity file, which provides sources of microbial toxicity and biodegradation data; CHEMFATE, a data file containing 25 categories of environmental fate and physical/chemical property information on commercially important chemical compounds; BIODEG, which contains experimental values relating to biodegradation subjects; and BIODEG summary, which provides summary evaluation

Falconer Biology Library

Environment Index

cwelborn@stanford.edu — Tue, 11 Nov 2008 10:45:57 -0800

Environment Index offers deep coverage in applicable areas of agriculture, ecosystem ecology, energy, natural resources, marine & freshwater science, geography, pollution & waste management, environmental technology, environmental law, public policy, social impacts, urban planning, and more. Environment Index contains more than 1,590,000 records from 1,500 domestic and international titles going back to the 1950s (including 960 active core titles) as well as 100 monographs.

Falconer Biology Library

Entrez

cwelborn@stanford.edu — Tue, 11 Nov 2008 10:39:40 -0800

Entrez searches the National Center for Biotechnology Information (NCBI) databases to provide integrated access to nucleotide and protein sequence data from over 160,000 species, along with three-dimensional protein structures, genomic mapping information, PubMed MEDLINE, and more. Sequence data are combined from various sources, including GenBank, EMBL, DDBJ, RefSeq, PIR-International, PRF, Swiss-Prot, and PDB.

Falconer Biology Library

EIS: Digests of Environmental Impact Statements

cwelborn@stanford.edu — Tue, 11 Nov 2008 10:34:49 -0800

EIS: Digests of Environmental Impact Statements indexes the hundreds of environmental impact statements issued by United States government agencies each year. For each environmental impact statement indexed in the database, an abstract includes a concise description of the project, sections on positive impact and negative consequences, and a list of legal mandates. The database indexes statements published from 1985 to the present.

Falconer Biology Library

Ecology Abstracts

nmayo@stanford.edu — Tue, 11 Nov 2008 10:22:13 -0800

Ecology Abstracts indexes journal articles in ecology and environmental science. Nearly 700 journals are indexed in full or in part, and the database indexes literature published from 1982 to the present. Coverage includes habitats, food chains, erosion, land reclamation, resource and ecosystems management, modeling, climate, water resources, soil, and pollution.

Falconer Biology Library

BioOne

nmayo@stanford.edu — Tue, 11 Nov 2008 10:17:26 -0800

BioOne is a full-text aggregation of bioscience research journals. Most are published by small societies and other not-for-profit organizations. Subjects covered by BioOne journals include ecology, evolution, environmental science, natural history, taxonomy, and systematics.

Falconer Biology Library

BIOBASE Knowledge Library (BKL)

nmayo@stanford.edu — Tue, 11 Nov 2008 09:53:05 -0800

BIOBASE Knowledge Library (BKL), combining the PROTEOME and TRANSFAC suites of databases, offers rich, high quality content and integrated analysis tools spanning gene regulation and pathways to fully annotated genomes. These database products offer a combination of computational and experimental data. PROTEOME is a comprehensive knowledge resource for the complete known proteomes of selected species, including humans. TRANSFAC compiles data on transcription factors, their experimentally-proven binding sites, and regulated genes.

Falconer Biology Library

Bacteriology Abstracts (Microbiology B)

nmayo@stanford.edu — Mon, 10 Nov 2008 16:02:48 -0800

Bacteriology Abstracts (Microbiology B) indexes journal articles in bacteriology. Over 400 journals are monitored for inclusion in this database, and years of coverage are 1982 to the present. With topics ranging from bacterial immunology and vaccinations to diseases of man and animals, the database provides access to clinical findings as well as pure bacteriology, biochemistry, and genetics.

Falconer Biology Library

ASFA: Aquatic Sciences and Fisheries Abstracts

nmayo@stanford.edu — Mon, 10 Nov 2008 15:52:39 -0800

ASFA: Aquatic Sciences and Fisheries Abstracts indexes literature in the field of aquatic resources, including aquaculture, aquatic pollution, brackish water environments, fisheries, marine biology, and oceanography. Input to ASFA is provided by an international network of information centers monitoring over 5,000 serial publications, books, reports, conference proceedings, translations and limited distribution literature.

Falconer Biology Library

Arctic & Antarctic Regions

nmayo@stanford.edu — Mon, 10 Nov 2008 15:40:46 -0800

Arctic & Antarctic Regions (AAR) is the world's largest collection of international polar databases. Coverage is multidisciplinary. A wide variety of sources are indexed including: scientific periodicals, monographs, proceedings of conferences and symposia, government reports, theses, dissertations, and books. Many are indexed only in AAR -- the best resource for research on cold regions anywhere, from temperate regions with cold winters to the Himalayas of Tibet."--NISC product factsheet

Falconer Biology Library

AGRICOLA

nmayo@stanford.edu — Mon, 10 Nov 2008 13:06:08 -0800

AGRICOLA serves as the catalog and index to the collections of the National Agricultural Library. The records describe publications and resources encompassing all aspects of agriculture and allied disciplines, including animal and veterinary sciences, entomology, plant sciences, forestry, aquaculture and fisheries, farming and farming systems, agricultural economics, extension and education, food and human nutrition, and earth and environmental sciences. AGRICOLA is organized into two data sets.

Falconer Biology Library

Biodiversity Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:44:34 -0800

Falconer Biology Library

Cell Biology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:42:06 -0800

Falconer Biology Library

Developmental Biology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:32:12 -0800

Falconer Biology Library

Ecology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:29:23 -0800

Falconer Biology Library

General Biology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:26:31 -0800

Falconer Biology Library

Genetics and Genomics Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:20:23 -0800

Falconer Biology Library

Insect Biology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:17:30 -0800

Falconer Biology Library

Microbiology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:13:25 -0800

Falconer Biology Library

Population Biology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 12:08:48 -0800

Falconer Biology Library

Wetlands Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 11:47:00 -0800

Falconer Biology Library

Neurobiology Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 10:43:01 -0800

Falconer Biology Library

Nucleic Acid Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 10:38:50 -0800

Falconer Biology Library

Protein Analysis Databases

nmayo@stanford.edu — Mon, 10 Nov 2008 10:25:05 -0800

Falconer Biology Library

Michael Newman

mnewman@stanford.edu — Mon, 10 Nov 2008 08:53:34 -0800

Falconer Biology Library

Sleep Science Databases

nmayo@stanford.edu — Fri, 07 Nov 2008 17:00:51 -0800

Falconer Biology Library

Neurobiology Encyclopedias

nmayo@stanford.edu — Thu, 06 Nov 2008 14:01:55 -0800

Falconer Biology Library

Microbiology Encyclopedias

nmayo@stanford.edu — Thu, 06 Nov 2008 13:45:39 -0800

Falconer Biology Library

EcoSal

nmayo@stanford.edu — Thu, 06 Nov 2008 12:39:24 -0800

EcoSal is a continually updated Web resource based on the classic ASM Press publication /Escherichia coli and Salmonella: Cellular and Molecular Biology/. Like its print-edition predecessors, EcoSal is a comprehensive archive of the entire corpus of knowledge on the enteric bacterial cell. EcoSal is comprised of several hundred modules of information and interpretation with links to sites containing tabular and pictorial presentations, as well as to active databases of primary research information.

Falconer Biology Library

POPLINE

nmayo@stanford.edu — Mon, 03 Nov 2008 15:39:00 -0800

POPLINE(POPulation information onLINE) contains citations with abstracts to scientific articles, reports, books, and unpublished reports in the field of reproductive health, population, family planning, and related health issues. POPLINE is maintained by the INFO Project at the Johns Hopkins Bloomberg School of Public Health/Center for Communication Programs and is funded by the United States Agency for International Development. (USAID). POPLINE contains nearly 360,000 records.

Falconer Biology Library

Table with images on Sleep Science Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 15:33:46 -0700

Falconer Biology Library

Table with images on Protein Analysis Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 15:28:43 -0700

One of many library books on protein analysis

Use Socrates to find printed or digital books or journals at Stanford.

Falconer Biology Library

Table with images on Population Biology Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 15:23:26 -0700

White-face capuchin (cebus capucinus), Gamboa, Panama. Photo courtesy of Jean Shen, Falconer Serials Specialist.

Use Socrates to find printed or digital books or journals at Stanford.

Falconer Biology Library

Table with images on Nucleic Acid Analysis Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 15:16:25 -0700

One of many library books on nucleic acid analysis

Use Socrates to find printed or digital books or journals at Stanford.

Falconer Biology Library

Table with images on Neurobiology Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 15:04:12 -0700

Use Socrates to find printed or digital books or journals at Stanford. Digital Journals available to the Stanford community are listed in Electronic Journals and Newspapers.

Falconer Biology Library

Table with images on Microbiology Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 14:50:03 -0700

A binucleate yeast cell stained for microtubules (red), DNA (blue) and GFP (green), marking one of the chromosomes as a lacI-GFP fusion protein.

Falconer Biology Library

Table with images on General Biology Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 14:35:32 -0700

Pineapple plant, Bocas del Toro, Panama. Photo courtesy of Jean Shen, Falconer Serials Specialist.

Use Socrates to find printed or digital books or journals at Stanford.

Falconer Biology Library

Table with images on Ecology Research Guide

nmayo@stanford.edu — Tue, 28 Oct 2008 09:32:19 -0700

Use Socrates to find printed or digital books or journals at Stanford. Digital Journals available to the Stanford community are listed in Electronic Journals and Newspapers.

Falconer Biology Library

Table with images on Developmental Biology Research Guide

nmayo@stanford.edu — Mon, 27 Oct 2008 16:27:19 -0700

One of many library books on developmental biology. This title is available full-text, online, as well as hardcopy.

Use Socrates to find printed or digital books or journals at Stanford.

Falconer Biology Library

Table with images on Wetlands Research Guide

nmayo@stanford.edu — Mon, 27 Oct 2008 15:53:29 -0700

Use Socrates to find printed or digital books or journals at Stanford. Digital Journals available to the Stanford community are listed in Electronic Journals and Newspapers.

Falconer Biology Library

PLANetWire

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:53:42 -0700

PLANetWire is a news service for journalists that provides information about reproductive health rights and services, maternal and child health, equality in education, women's empowerment, youth participation and a healthy environment. www.PLANetWIRE.org provides reporters with story ideas, facts and figures, expert spokespeople, information from organizations and government agencies, and links to blogs to provide background on these issues.

Falconer Biology Library

Population Reference Bureau

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:51:53 -0700

The Population Reference Bureau provides information about population, health, and the environment. PRB focuses work around four themes: Reproductive Health and Fertility; Children and Families; Population and the Environment; and Population Futures, including Aging, Inequality and Poverty, Migration and Urbanization, and Gender. The website presents demographic data for the United States and over 200 other countries.

Falconer Biology Library

United Nations Population Division

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:50:03 -0700

The Population Division is an international agency that prepares high-quality documentation regarding population issues. The agency’s website provides access to these reports and to collections of population data.

Falconer Biology Library

International Human Dimensions Programme on Global Environmental Change

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:41:24 -0700

The International Human Dimensions Programme on Global Environmental Change (IHDP) is an international, interdisciplinary science programme, dedicated to promoting, catalysing and coordinating research, capacity-development and networking on the human dimensions of global environmental change. This site provides information about the organization and its activities.

Falconer Biology Library

International Union for the Scientific Study of Population

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:30:40 -0700

The IUSSP is a non-profit worldwide association of population specialists that promotes demography as a science and aims to draw attention to population problems. The IUSSP website includes a comprehensive list of links to websites on topics related to population.

Falconer Biology Library

Population-Environment Research Network

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:29:01 -0700

The Population-Environment Research Network seeks to advance academic research on population and the environment by promoting online scientific exchange among researchers from social and natural science disciplines worldwide. Membership is free and open to those who work on population and environment issues. The site provides access to the PERN eLibrary, a reference tool for classic population-environment literature, journal articles, conference and working papers, relevant data sets, and educational resources.

Falconer Biology Library

United Nations Population Fund

cwelborn@stanford.edu — Fri, 24 Oct 2008 14:23:02 -0700

The United Nations Population Fund (UNFPA) is an international development agency that promotes reproductive health and gender equality. The UNFPA website presents a wide array of information about human population and health, including short summaries of population issues, access to the annual publication, State of World Population, summaries of national population and development indicators, and ordering information for UNFPA publications.

Falconer Biology Library

Wetlands and Aquatic Environments Web Resources

nmayo@stanford.edu — Fri, 24 Oct 2008 11:13:56 -0700

Falconer Biology Library

Sleep Science Web Resources

nmayo@stanford.edu — Fri, 24 Oct 2008 11:11:26 -0700

Falconer Biology Library

Protein Analysis Web Resources

nmayo@stanford.edu — Fri, 24 Oct 2008 11:08:06 -0700

Falconer Biology Library

Population Biology Web Resources

nmayo@stanford.edu — Fri, 24 Oct 2008 11:04:33 -0700

Falconer Biology Library

Nucleic Acid Analysis Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 16:52:18 -0700

Falconer Biology Library

Neurobiology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 16:49:21 -0700

Falconer Biology Library

Microbiology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 16:45:58 -0700

Falconer Biology Library

Genetics and Genomics Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 16:19:51 -0700

Falconer Biology Library

General Biology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 16:16:16 -0700

Falconer Biology Library

Developmental Biology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 16:11:18 -0700

Falconer Biology Library

Cell Biology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 15:48:09 -0700

Falconer Biology Library

Insect Biology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 15:26:50 -0700

Falconer Biology Library

Ecology Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 15:10:47 -0700

Falconer Biology Library

Biodiversity Web Resources

nmayo@stanford.edu — Thu, 23 Oct 2008 09:20:12 -0700

Falconer Biology Library

Databases in the Life Sciences

nmayo@stanford.edu — Wed, 22 Oct 2008 11:37:47 -0700

This alphabetical list describes and provides access to databases that are used frequently by faculty, staff, and students in the biological sciences. KEY SITE designates the most frequently used of these. Following the list are annotations on each database. Many of these databases, along with other resources, are grouped by subject area in the RESEARCH GUIDES.

Falconer Biology Library

Three-minute Science

mnewman@stanford.edu — Mon, 20 Oct 2008 12:40:21 -0700

Short Attention Span Science Theater presents short films on topics in ecology and conservation.

Falconer Biology Library

Chemistry Nobel Prize Awarded for Glowing Protein Work

nmayo@stanford.edu — Thu, 16 Oct 2008 15:38:59 -0700

The Nobel Prize for Chemistry for 2008 is awarded to scientists who discovered a green, fluorescent protein in the jellyfish, Aequorea victoria. Check out the Falconer Research Guide on Genetics and Genomics for a photo showing the use of this protein in research with neurospora.
Read article on prize winners

Falconer Biology Library

Table with images on Insect Biology Research Guide

nmayo@stanford.edu — Thu, 16 Oct 2008 14:58:20 -0700

Falconer Biology Library

Archived List of New Books

nmayo@stanford.edu — Thu, 16 Oct 2008 11:41:43 -0700

Books from the last 6 weeks are listed here. Earlier lists are available in the library.

Acquisitions for the week of November 16, 2009

MONOGRAPHS

ABC transporters in microorganisms: research, innovation and value as targets against drug resistance. Edited by Ponte-Sucre, Alicia. 2009.

Falconer Biology Library

Table with images on Cell Biology Research Guide

nmayo@stanford.edu — Thu, 16 Oct 2008 10:38:09 -0700

The mitotic spindle of a human U2OS cell in metaphase, stained for microtubules (green), DNA (blue) and gamma-tubulin (red). Gamma-tubulin is a specialized tubulin limited to the centrosomes at the poles of the spindle.

Falconer Biology Library

Table with images on Biodiversity Research Guide

nmayo@stanford.edu — Thu, 16 Oct 2008 09:37:24 -0700

Denali National Park & Preserve, Alaska

Use Socrates to find printed or digital books or journals at Stanford. Digital Journals available to the Stanford community are listed in Electronic Journals and Newspapers.

Falconer Biology Library

Table with images on Genetics Research Guide

nmayo@stanford.edu — Wed, 15 Oct 2008 13:28:14 -0700

Neurospora is a filamenous model fungus widely used in genetic and biochemical investigations. George Beadle and Edward Tatum of Stanford University used Neurospora in 1941 for demonstrating that genes specify enzymes, which carry out biochemical reactions in the cell.

Falconer Biology Library

Wetlands and Aquatic Environments Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:25:41 -0700

Falconer Biology Library

Sleep Science Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:22:53 -0700

Falconer Biology Library

Protein Analysis Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:19:46 -0700

Falconer Biology Library

Population Biology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:16:26 -0700

Falconer Biology Library

Nucleic Acid Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:11:40 -0700

Falconer Biology Library

Neurobiology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:08:19 -0700

Falconer Biology Library

Microbiology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 12:02:38 -0700

Falconer Biology Library

Insect Biology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:56:40 -0700

Falconer Biology Library

Genetics and Genomics Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:52:57 -0700

Falconer Biology Library

General Biology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:50:52 -0700

Falconer Biology Library

Ecology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:46:54 -0700

Falconer Biology Library

Developmental Biology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:43:06 -0700

Falconer Biology Library

Biodiversity Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:32:13 -0700

Falconer Biology Library

Cell Biology Articles

nmayo@stanford.edu — Wed, 15 Oct 2008 11:13:43 -0700

Falconer Biology Library

Henry Stewart Talks Biomedical and Life Sciences Collection

nmayo@stanford.edu — Wed, 15 Oct 2008 11:02:50 -0700

Falconer Biology Library has added a subscription to the Henry Stewart Talks Biomedical and Life Sciences Collection, and the talks are available from Stanford IP addresses at this URL: http://www.hstalks.com/access

Falconer Biology Library

Revolution on the range : the rise of a new ranch in the American west

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:58:18 -0700

Falconer Biology Library

Theory and mathematical methods for bioinformatics

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:52:25 -0700

Falconer Biology Library

Tree atlas of Namibia

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:44:53 -0700

Falconer Biology Library

Visualization in medicine and life sciences

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:37:49 -0700

Falconer Biology Library

World sustainable development outlook 2007: knowledge management and sustainable development in the 21st century

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:34:42 -0700

Falconer Biology Library

Bears: a brief history

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:28:06 -0700

Falconer Biology Library

Architecture by birds and insects : a natural art

cwelborn@stanford.edu — Mon, 13 Oct 2008 15:25:59 -0700

Falconer Biology Library

View New Books Bibliography

nmayo@stanford.edu — Mon, 13 Oct 2008 09:10:03 -0700

View New Books Bibliography

Falconer Biology Library

Trace elements as contaminants and nutrients: consequences in ecosystems and human health

nmayo@stanford.edu — Fri, 10 Oct 2008 09:13:08 -0700

Falconer Biology Library

R Programming for bioinformatics

nmayo@stanford.edu — Fri, 10 Oct 2008 09:08:27 -0700

Falconer Biology Library

Neurobiology of the parental brain

nmayo@stanford.edu — Fri, 10 Oct 2008 09:05:32 -0700

Falconer Biology Library

Lecture notes on computational structural biology

nmayo@stanford.edu — Fri, 10 Oct 2008 08:58:00 -0700

Falconer Biology Library

Insect conservation and islands

nmayo@stanford.edu — Fri, 10 Oct 2008 08:53:18 -0700

Falconer Biology Library

Horizontal gene transfer in the evolution of pathogenesis

nmayo@stanford.edu — Fri, 10 Oct 2008 08:47:07 -0700

Falconer Biology Library

Archaea: new models for prokaryotic biology

nmayo@stanford.edu — Fri, 10 Oct 2008 08:40:57 -0700

Falconer Biology Library

New Acquisitions

nmayo@stanford.edu — Mon, 06 Oct 2008 20:07:18 -0700

New Books The new book display is located next to the media shelves, in the enclave between the second and third balconies. It is changed every Monday afternoon between 4:00 and 5:00 pm. The new books are only available for in-house use during the week they are on display. Patrons who wish to place a hold on any of the new books may go to the Socrates record by clicking on the title.

Falconer Biology Library

Dissertations and Theses

nmayo@stanford.edu — Wed, 17 Sep 2008 13:57:38 -0700

Stanford Dissertations and Theses

Digital Format

Falconer Biology Library

Course Reserves

nmayo@stanford.edu — Wed, 17 Sep 2008 13:53:50 -0700

Course Reserves are items which are in high demand for a particular course. Falconer Library provides reserve services for the Department of Biology and for selected courses in Psychology, Applied Physics, Neurobiology, and the Program in Human Biology. Most Human Biology course reserves are at the Green Library.

FOR STUDENTS

Falconer Biology Library

Library Instruction

nmayo@stanford.edu — Wed, 17 Sep 2008 13:47:56 -0700

Falconer Biology Library offers tours of the facility by appointment for any group or individual. Preference is given to persons who are affiliated with Stanford University. For large classes, a series of tours for groups of ten or fewer persons may be required.

By appointment, the library also offers training sessions in the use of the library; in searching Socrates, BIOSIS, SciSearch, and other library databases; and in finding literature in the life sciences. A training session may be combined with a tour of the library or offered separately.

Falconer Biology Library

Reference

nmayo@stanford.edu — Wed, 17 Sep 2008 13:42:00 -0700

Library staff are available during reference hours to provide help with library research, instruct patrons on the use of the library, and to assist in finding and accessing information not owned by the library. Online search services are available by appointment. Tours of the library, group instruction, and specialized training in biological information sources can be arranged by sending a message to falconerlibrary@stanford.edu or by inquiring at the Circulation Desk (650) 723-1528.

Falconer Biology Library

Nucleic Acids Research Journal

cwelborn@stanford.edu — Fri, 05 Sep 2008 16:10:27 -0700

Published by Oxford Journals Online, Nucleic Acids Research Journal gives access to full text articles from 1996 to the current issue, with abstracts available as far back as 1975, as well as the annual database issue.

Falconer Biology Library

Entrez Nucleotide

cwelborn@stanford.edu — Fri, 05 Sep 2008 16:08:03 -0700

The Nucleotide database contains records for all Entrez Nucleotide sequences that are not found within the Expressed Sequence Tag (EST) or Genome Survey Sequence (GSS) divisions of GenBank. These include sequences from all remaining divisions of GenBank, NCBI Reference Sequences (RefSeqs), Whole Genome Shotgun (WGS) sequences, Third Party Annotation (TPA) sequences, and sequences imported from the Entrez Structure database.

Falconer Biology Library

RNase P Database

cwelborn@stanford.edu — Fri, 05 Sep 2008 16:06:24 -0700

The RNase P Database is a collection of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and additional information.

Falconer Biology Library

SILVA rRNA Database

cwelborn@stanford.edu — Fri, 05 Sep 2008 16:04:48 -0700

The SILVA databases are maintained by the Microbial Genomics Group at the Max Planck Institute (MPI) for Marine Microbiology, in cooperation with the Department of Microbiology at the Technical University of Munich and Ribocon. The web resource provides quality checked and regularly updated databases of aligned SSU (small subunit) and LSU (large subunit) ribosomal RNA (rRNA) sequences. These databases can be used for rapid rRNA sequence retrieval, phylogenetic analysis, and the design of probes and primers for diversity analysis. They are fully compatible with the software package ARB.

Falconer Biology Library

RNA Modification Database

cwelborn@stanford.edu — Fri, 05 Sep 2008 16:02:47 -0700

The RNA Modification Database is an updated and comprehensive listing of post-transcriptionally modified nucleosides from RNA. It is searchable by various parameters including base type and RNA source.

Falconer Biology Library

ExPASy Translate Tool

cwelborn@stanford.edu — Fri, 05 Sep 2008 16:00:30 -0700

The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures. ExPASy Translate is a tool that translates a DNA or RNA sequence to a protein sequence.

Falconer Biology Library

Xenbase: a Xenopus Web Resource

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:47:59 -0700

Xenbase is a database filled with information on the developmental biology of the frog, Xenopus.

Falconer Biology Library

Sea Urchin Embryology

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:45:40 -0700

The sea urchin embryology tutorial is great for the undergraduate level student and teachers. It has basic but thorough information on sea urchin embryology, as well as ideas for labs and activities.

Falconer Biology Library

Amphibian Embryology Tutorial

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:37:19 -0700

The amphibian embryology tutorial takes you through various stages, including oogenesis, cleavage, gastrulation and neurulation. Each stage provides background information as well as diagrams and pictures. There is also an extensive glossary.

Falconer Biology Library

Visible Embryo

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:32:31 -0700

The visible embryo provides information on human development from conception to birth that can be used by students. Accompanying the pictures and information regarding normal development are pictures and information about abnormal embryonic development.

Falconer Biology Library

Virtual Embryo

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:29:54 -0700

This tutorial is designed as an addition to developmental biology lectures and introduces you to the dynamics of embryonic growth. It includes extensive information on C. elegans, Xenopus, Drosophila, chick, fish and the sea urchin.

Falconer Biology Library

Developmental Biology Online

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:22:17 -0700

The developmental biology online website developed for a course at the University of Guelph gives great outlines and photographs on various subjects in developmental biology. Some of which include cleavage, gametogenesis, gastrulation and information on various animals.

Falconer Biology Library

International Journal of Developmental Biology

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:18:58 -0700

The official website for the International Journal of Developmental Biology allows searching of abstracts, full text for some articles in back issues, and special issues covering a variety of topics in developmental biology.

Falconer Biology Library

Virtual Library-Developmental Biology

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:15:20 -0700

This portion of the Society for Developmental Biology website contains an extensive virtual library, with links to various subjects including early development, morphogenesis, cell lineage and patterns, and various organisms. Each link leads to listings of websites for various labs, each including research and techniques regarding a specific topic.

Falconer Biology Library

Atlas of Developmental Abnormalities

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:05:49 -0700

This searchable atlas offers numerous pictures of laboratory animals with developmental abnormalities at various stages of development. The animals pictured are rats, rabbits and mice.

Falconer Biology Library

United Nations Population Information Network (POPIN)

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:02:48 -0700

POPIN is a guide to United Nations population information. It provides population estimates and projections for every country, including birth rates, death rates, and other demographic indicators. It also includes links to publications, organizations, and information about conferences on world population issues.

Falconer Biology Library

Population Index

cwelborn@stanford.edu — Fri, 05 Sep 2008 15:00:54 -0700

Population Index is a reference tool to population literature. It includes a bibliography of recently published books, journal articles, and working papers on population topics. It also provides a searchable database with 46,035 abstracts of demographic literature published in Population Index in the period 1986-2000.

Falconer Biology Library

Internet Directory for Botany

cwelborn@stanford.edu — Fri, 05 Sep 2008 14:57:45 -0700

This Internet Directory for Botany contains an extensive listing of links pertaining to botany, including multiple on the subject of plant ecology.

Falconer Biology Library

Stream and Fish Data for the Northwest

cwelborn@stanford.edu — Fri, 05 Sep 2008 14:52:40 -0700

Stream Net focuses on fisheries and other stream data in the Pacific Northwest, more specifically, the Columbia River Basin. There is extensive online fish data including a library, photographs and GIS data.

Falconer Biology Library

Coral Reef Database

cwelborn@stanford.edu — Fri, 05 Sep 2008 14:33:01 -0700

The coral reef database is a collection of online resources for researchers and professionals within the coral reef field. Topics included are management, research, monitoring, conservation and education.

Falconer Biology Library

Wetlands Regulation Center

cwelborn@stanford.edu — Fri, 05 Sep 2008 14:30:52 -0700

The Wetlands Regulation Center offers information about laws, policies and regulations according to the Clean Water Acts regarding wetlands.

Falconer Biology Library

Amazonian Fishes

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:49:06 -0700

Amazing photographs of Amazonian fish and their surroundings supplement this website. Also included are many ecological aspects of the Amazon, including waters, communities, plants and forests.

Falconer Biology Library

Birds of Stanford

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:34:06 -0700

The birds of Stanford website is prepared by Stanford alumni and contains photos, artwork, essays and species lists about the 125 species of birds found on campus.

Falconer Biology Library

Bill’s Wildlife Sites

nmayo@stanford.edu — Thu, 04 Sep 2008 15:31:49 -0700

Wildlife Web Links consists of various sites for wildlife biologists including sites about specific animals and organizations.

Falconer Biology Library

Animal Info – Information on Endangered Mammals

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:29:56 -0700

Information about endangered mammals including many pictures is included on this website. It is searchable by individual species or species group. Each animal page includes a profile, status and trends, data on biology and ecology and more references.

Falconer Biology Library

American Fisheries Society

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:11:33 -0700

AFS website offers information about the society, education, jobs, publications and an in-depth list of links.

Falconer Biology Library

Envirolink: The Online Environmental Community

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:09:33 -0700

This online environmental community provides numerous Internet resources that pertain to the environment as well as news headlines and a discussion forum.

Falconer Biology Library

US Long Term Ecological Research Network

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:07:11 -0700

The LTER Network has a website where scientists and students can compare research that can be used in long-term projects. Included on the site are directories, bibliographies and affiliations.

Falconer Biology Library

World Ecology

cwelborn@stanford.edu — Thu, 04 Sep 2008 15:02:58 -0700

This website supported by WorldNews.com provides up to date news about Ecology. Some included topics are earthquakes, forestry, global warming, science and weather.

Falconer Biology Library

Ecology WWW Page

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:52:42 -0700

The Ecology web links site offers thousands of Ecology links sorted alphabetically about a multitude of subjects, languages and countries.

Falconer Biology Library

Environmental Yellow Pages-Ecology

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:50:36 -0700

The Ecology portion on the Environmental Yellow Pages website is helpful and contains multiple subjects including Aquatic Ecology, Ecology Research Centers, Ecosystems, Restoration Ecology and Wildlife Ecology. For each subject there is an extensive listing on links for information and resources.

Falconer Biology Library

National Gap Analysis Program (USGS)

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:48:34 -0700

The Gap Analysis Program is part of the USGS, and determines the extent to which native animal and plant species are protected. The website includes information on ongoing projects, data and reports, meetings and project resources.

Falconer Biology Library

National Center for Ecological Analysis and Synthesis (NCEAS)

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:44:54 -0700

The NCEAS website includes information about different research projects in the field of ecology and their results. There is also a portion that discusses the role of informatics in the field of ecology.

Falconer Biology Library

Virtual Library of Ecology and Biodiversity

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:42:23 -0700

This virtual library is a portion of the Center for Conservation Biology Network that reviews Internet Information regarding Ecology. The Internet resources are then broken down into categories that include lists of links.

Falconer Biology Library

National Service Center for Environmental Publications (NSCEP)

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:40:18 -0700

NSCEP/NEPIS is the U.S. Environmental Protection Agency’s gateway to free digital and paper publications. More than 7,000 print publications are available through the National Service Center for Environmental Publications (NSCEP), and 27,000 digital publications are available through the related National Environmental Publications Internet Site (NEPIS).

Falconer Biology Library

The Global Invasive Species Team

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:37:59 -0700

The Global Invasive Species Team is part of The Nature Conservancy's response to abating the damage caused to native biodiversity by the human-facilitated introduction of non-native, harmful invasive species. This web site provides many resources designed to help conservationists deal most effectively with invasive species.

Falconer Biology Library

The Ecological Society of America (ESA)

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:35:03 -0700

The ESA website promotes the Science of Ecology and includes career information, meetings and various publications. Also included are various links to journals, archives and listservs.

Falconer Biology Library

Peterson’s Guides

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:31:30 -0700

This educations resource has information about colleges/universities, graduate programs, test preparation, essay and resume services, financial aid and distance learning.

Falconer Biology Library

Infomine: Scholarly Internet Resource Collections

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:15:52 -0700

Infomine has over 100,000 searchable, academically valuable resources, most specifically a section on biological, agricultural and medical sciences. After searching for a specific term, Infomine retrieves a myriad of databases and sources pertaining to that term.

Falconer Biology Library

On-line Biology Book

cwelborn@stanford.edu — Thu, 04 Sep 2008 14:07:32 -0700

This E-Book contains over 50 chapters with general biology information. Some of the chapter titles are cells, proteins, thermodynamics, reactions, plants and diversity. The end of each chapter contains learning objectives, terms, review questions and links.

Falconer Biology Library