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Basic Sciences Guide
by Rae Jeffers Last Updated Apr 16, 2024 15 views this year

BioToolKit This link opens in a new window An annotated directory of links to online molecular biology and neuroinformatics resources, including basic research tools as well as advanced tools enabling integrated, multi-level analysis of the genome, transcriptome, and proteome. Divided into four sections: Nucleic Acid Analysis, Genomics Resources, Protein Structural Imaging and Analysis, and Neuroinformatics.

Cold Spring Harbor Protocols Interactive online methods database developed by Cold Spring Harbor Laboratory. Includes protocols in cell and molecular biology, genetics, protein science, imaging, and bioinformatics.

Current Protocols This link opens in a new window Includes step-by-step protocols with annotations; alternate and support protocols to accommodate different equipment and desired results; materials lists for each protocol; and more. Access is provided only to full-text content published during the time the Library actively subscribed to each title; as of January 1, 2014, there is no current subscription.

Ensembl Genome Browser Ensembl provides automatic annotation to human genome data. A central element of the Ensembl project is openness; all data and code are freely available.

IEEE Xplore This link opens in a new window Online delivery system that provides full text access to all of the IEEE (Institute of Electrical and Electronics Engineers) and IEE (Institution of Electrical Engineers) transactions, journals, magazines and conference proceedings published since 1988 and all current IEEE standards. IEEE Xplore contains more than 450,000 full-text articles and papers in over 12,000 individual publications. Previously known as IEL Online. Provided by UT Southwestern and the UT System Libraries.

Methods in Enzymology (ScienceDirect) Browse the individual volumes going back to 1955, or search across the collection by title, author, abstract, and keyword. ISSN: 0076-6879.
Publication Date: 1995 - Present

NCBI BLAST Basic Local Alignment Search Tool (BLAST).

NCBI Databases This link opens in a new window Quick links to the National Center for Biotechnology Information's literature, nucleotide, genome, sequence analysis, data mining, population, taxonomy and other databases.

NCBI Gene Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode. Replaces LocusLinks.
NCBI Handbook, 2002-2005 (NCBI) Provides a cohesive approach to describing the databases and search engines as well as significant information on how the databases work or can be leveraged for bioinformatics research on a larger scale. The intended audience is the growing number of scientists and students who would like a more in-depth guide to NCBI resources. Focused on the relatively stable information about each research, this resource is not a point-and-click guide; a certain amount of biological knowledge is assumed. Available from NCBI Bookshelf.
PharmGKB The Pharmacogenomics Knowledgebase (PharmGKB) is an NIH-funded resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships.

Protein Data Bank This link opens in a new window The Protein Data Bank (PDB), operated by the Research Collaboratory for Structural Bioinformatics (RCSB), is an international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR. Retrieve structure files, search for proteins with the PDB ID or with keywords, contribute new structure data, find entries awaiting release, and more.

PubChem PubChem contains the chemical structures of small organic molecules and information on their biological activities and is searchable via PubChem Substance, PubChem Compound, PubChem Bioassay and PubChem Structure Search.
RasMol RasMol is a free program which displays molecular structure and is available for PC/Windows, MacIntosh, Unix, and VAX VMS platforms. RasMol is an educational tool for showing the structure of DNA, proteins, and smaller molecules that produces colored three-dimensional images. The site provides file downloads, tutorials, a gallery of images, a discussion list, and more.
RasTop proteins, nucleic acids, and small molecules. RasTop offers a user-friendly graphical interface around "RasMol molecular engine." This site is limited to downloads and technical notes.

Reaxys + Reaxys Medicinal Chemistry This link opens in a new window Reaxys contains an extensive repository of experimentally validated data that chemists need, such as structures, reactions (including multi-step reactions), and physical properties and provides relevant data not found elsewhere, drawn from source publications carefully selected for their importance and relevance to synthetic chemists. The Reaxys Medicinal Chemistry component includes comprehensive pharmacokinetic, efficacy, toxicity, safety, and metabolic profiles, as well as tools for hit set assessment, including an interactive heatmap and bioactivity tables. Includes Beilstein, Gmelin, and Patent Chemistry Database content, as well as information on inorganic and organometallic substances. Provided jointly by UT Southwestern Medical Center Library and the Department of Biochemistry.
Repbase (Genetic Information Research Institute) This link opens in a new window A database of prototypic sequences representing repetitive DNA from different eukaryotic species, which is being used in genome sequencing projects worldwide as a reference collection for masking and annotation of repetitive DNA (e.g. by RepeatMasker or CENSOR).

Science Signaling: Signal Transduction Knowledge Environment A Web site and online journal devoted to the topic of cell signaling. Enables experts and novices in cell signaling to find, organize, and utilize information relevant to processes of cellular regulation. Provides access to the full text of current research relating to biological signal transduction, which is published in participating journals. Also features perspectives, reviews, and protocols; teaching resouces; and links to other online resources. Published weekly by the editors of Science and the technical staff of Stanford University's HighWire Press. Provided by UT Southwestern and the UT System Libraries.

ScienceDirect® This link opens in a new window Contains full-text journals in the life, physical, medical, technical, and social sciences. Also contains abstracts from non-Elsevier core journals in the major scientific disciplines and the ability to link directly to full-text articles licensed through other science, technology, and medicine publishers. Includes Scirus, a Web search engine that focuses on scientific content only and searches both Web and proprietary databases for information that complements ScienceDirect content. Provided by UT Southwestern and the UT System Libraries.

SciFinder Web FAQ (UT Southwestern) Provides graphical access to Chemical Abstracts Service and MEDLINE. Covers the full spectrum of chemical and biomedical information, including biochemistry, organic/inorganic chemistry, and chemical engineering/applied chemistry. Substructure and reaction searching are also available. Access to SciFinder is restricted to affiliated faculty, staff, and students of UT Southwestern, and the UT Southwestern University Hospitals. Provided by UT Southwestern and the UT System Libraries.
SciVee A social community for researchers of all levels that encourages sharing published research through online video presentations. Members can see and hear colleagues describe their research, join specific interest communities, participate in discussions, and create a comprehensive multimedia representation of their own research.

Scopus This link opens in a new window Multidisciplinary scientific database covering 25 million abstracts from over 14,000 titles across 4,000 publishers. Includes journal articles, patents, conference proceedings, and Web sites in the physical sciences, health sciences, life sciences, and social sciences. Covers journals from 1966 to the present.
Web of Science This link opens in a new window Covers more than 12,000 high-impact journals in the sciences, social sciences, and arts and humanities, as well as international proceedings coverage for over 150,000 conferences. Includes cited reference searching and Citation Maps (i.e., a graphical representation that shows citation relationships between a paper and other papers). Access is provided to the Science Citation Index Expanded® (1900-present), Social Sciences Citation Index® (1900-present), Arts & Humanities Citation Index® (1975-present), Conference Proceedings Citation Index: Science Edition (1990-present), and Conference Proceedings: Social Sciences & Humanities Edition (1990-present). Provided by UT Southwestern and the UT System Libraries.

C. Elegans II, 2nd ed. (NCBI) by Donald Riddle Defines current status of studies of the cells and genes of the nematode C. elegans, providing a detailed molecular explanation of how development is regulated and how the nervous system specifies varied aspects of behavior. Intended for worm studies investigators and other cellular and molecular biology researchers. Available from NCBI Bookshelf.
ISBN: 0879695323
Publication Date: 1998-01-01
Genomes, 2nd ed. (NCBI) by Terence A. Brown Covers molecular genetics from the genomics perspective and incorporates the major advances made in the past three years. Includes the sequencing of the human genome, characterization of genome expression and replication processes, and transcriptomics and proteomics. Available from NCBI Bookshelf.
ISBN: 0471250465
Publication Date: 2002-07-12
Metagenomics: Sequences from the Environment (NCBI) by National Center for Biotechnology Information (US) This book contains these chapters: Acid Mine Drainage Biofilm, Waseca County Farm Soil, Whale Fall Community, Methane-Oxidizing Archaea, Human Fecal Virus, Sargasso Sea Marine Microbial Metagenome, Human Distal Gut Microbiome, Enhanced Biological Phosphorus Removal (EBPR) Sludge Community, Mouse Gut Microbiota Metagenome. Available from NCBI Bookshelf.
Publication Date: 2006
Methods in Enzymology (ScienceDirect) Browse the individual volumes going back to 1955, or search across the collection by title, author, abstract, and keyword. ISSN: 0076-6879.
Publication Date: 1995 - Present
Mouse Genetics: Concepts and Applications (Jackson Laboratory) by Lee M. Silver This classic 1995 text, which is no longer in print, has been made available online by the Jackson Laboratory in Bar Harbor, Maine. It includes the full text, tables, figures, and references. There is a table of contents, but no index or search options.
Publication Date: 1995

NCBI Handbook, 2002-2005 (NCBI) Provides a cohesive approach to describing the databases and search engines as well as significant information on how the databases work or can be leveraged for bioinformatics research on a larger scale. The intended audience is the growing number of scientists and students who would like a more in-depth guide to NCBI resources. Focused on the relatively stable information about each research, this resource is not a point-and-click guide; a certain amount of biological knowledge is assumed. Available from NCBI Bookshelf.

Sequence - Evolution - Function: Computational Approaches in Comparative Genomics (NCBI) by Eugene V. Koonin; Michael Y. Galperin Introduces the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. Provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Available from NCBI Bookshelf.
ISBN: 1402072740
Publication Date: 2002-11-30

American Association of University Women (AAUW) Fellowships, Grants, and Awards for U.S. and International Women Scholars The American Association of University Women (AAUW) Educational Foundation supports aspiring scholars around the globe, teachers and activists in local communities, women at critical stages of their careers, and those pursuing professions where women are underrepresented by providing more than 278 fellowships, grants, and special awards each year.
ADVANCE: Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers Develop systemic approaches to increase the representation and advancement of women in academic science and engineering careers, thereby contributing to the development of a more diverse science and engineering workforce. Members of underrepresented minority groups and individuals with disabilities are especially encouraged to apply. Proposals that address the participation and advancement of women with disabilities and of women from underrepresented minority groups are encouraged.
Grants Information Service (Dallas Public Library) Offers information on foundations, grants, proposal writing, fundraising, and nonprofit management. The Dallas Public Library is a cooperating organization with the Foundation Center and provides access to their publications.
Find Funding (NIH Guide for Grants and Contracts) The official publication for the National Institutes of Health's (NIH) grant policies, guidelines, and funding opportunities. Updated daily.
Foundation Center Connects nonprofits and the grantmakers supporting them to a comprehensive database on U.S. grantmakers and their grants as well as research, education, and training programs designed to advance philanthropy at every level. Some training materials for grant writing are available for free, but a subscription is required to use the database. (Note: The Dallas Public Library provides access at the Central Library location.)
Funding Information Center, Texas Department of State Health Services The Funding Information Center's mission is to help organizations in Texas pursue public health funding opportunities by disseminating information through the Funding Alert and the center's Web site. Services are limited to clients living in Texas.
Graduate Women In Science (GWIS) National Fellowships Program Offers grants and fellowship opportunities to women enrolled as graduate students or engaged in postdoctoral or early-stage junior faculty academic research in the natural sciences. Applicants must demonstrate financial need for continuation or completion of their research, but they are not required to be GWIS members. There are no citizenship requirements.
Guide for Writing a Funding Proposal Assists people in gaining funds for projects that provide a worthwhile social service. Focuses on the development of meaningful cooperative relationships  with funding agencies, community organizations, and the populations being served. Created by S. Joseph Levine, Ph.D., of Michigan State University, East Lansing, Michigan.
International Cancer Research Partnership Database The International Cancer Research Portfolio (ICRP) is a database of information on cancer research awards from three leading funding organizations: the US National Cancer Institute (NCI), the US Congressionally-Directed Medical Research Programs (CDMRP), and the UK National Cancer Research Institute (NCRI). These awards may be searched by cancer type, broad scientific area, location (i.e., state or country), funding organization, and recipient institutions.
K Kiosk: NIH Career Development Awards Contains information about NIH career development awards for all faculty research stages. Some award types give information for individuals at specific institutes.
National Medical Fellowships A non-profit organization dedicated to increasing the number of underrepresented minority physicians in the United States by providing financial support and other incentives to underrepresented minority medical students. Offers fellowship programs to minority medical students that provide the opportunity to study or serve in internships within various areas, including biomedical research, community medicine, pediatric nutrition, and substance abuse research and treatment. Priority is given to second- and third-year students, and fellowships are not renewable.
NIH Grants & Funding Opportunities - Home NIH Grants and Funding website home page. To stay current in your areas of interest, you can set up email alerts.
NIH Guide for Grants and Contracts (Tables of Contents Alerts) Each week the NIH transmits via LISTSERV email the Table of Contents (TOC) information for that week's issue of the NIH Guide for Grants and Contracts. Associated with each TOC entry is the WWW address (URL) for each Guide article.
NIH Resources for New Investigators Describes current policies and resources that new investigators can use to understand and work with the NIH, including hints that might be useful in constructing a first application for NIH support. From NIH's Office of Extramural Research.
Postdoctoral Training in the NIH Intramural Research Program Postdoctoral program for recent graduates to train at the NIH. Opportunities are available for both U.S. citizens and international applicants.
Tips & Tools - Writing Center at UNC-Chapel Hill Offers a variety of materials about aspects of the writing process, including using statistics in writing, avoiding plagiarism, dealing with writing anxiety, using commas, writing grant proposals and dissertations, and much more. Get tips for your application essay and a head start on future academic writing. Demos require the latest version of Flash Player. Provided by the University of North Carolina at Chapel Hill.
Writing a Successful Grant Proposal (Minnesota Council on Foundations) A thorough explanation of what to do and what to avoid when writing a grant proposal and what to expect during the application process. Provided by the Minnesota Council on Foundations.

eMouseAtlas (EMAP) Includes high-resolution, annotated images of histologic sections of a developing embryo from 5.5 to 9 days after conception. Also links to a gene expression data bank. From the Medical Research Council's Human Genetics Unit, Edinburgh, U.K.

FlyBase: A Database of Drosophila Genes & Genomes This link opens in a new window FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. It includes data from the Drosophila Genome Projects and data curated from the literature. FlyBase is a joint project with the Berkeley and European Drosophila Genome Projects.
Gene Structural Annotation: Arabidopsis thaliana Genome This link opens in a new window Provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. In addition, pages on news, information on the Arabidopsis Genome Initiative (AGI), Arabidopsis lab protocols, and useful links are provided.

Genetic Maps of the Rat Genome Includes pictures of genetic linkage maps of the rat, which are available in PDF, PICT, or PostScript formats. The maps contain 4,786 markers, and a table listing the number of markers by cross, type, and chromosome may be viewed or downloaded. Produced by the Whitehead Institute for Biomedical Research/Massachusetts Institute of Technology Center for Genome Research.
Human Genetic Diseases Research (The Jackson Laboratory) Supports and provides access to a variety of tools: Mouse Phenome Database, Mouse Genome Informatics, International Mouse Strains Resources, Mouse Resources, and Informational Resources. From the Jackson Laboratory.
Mitelman Database Chromosome Aberrations and Gene Fusions in Cancer The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman in collaboration with Bertil Johansson and Fredrik Mertens.
Mouse Genome Informatics MGI resource comprises the Mouse Genome Database (MGD), the Gene Expression Database (GXD), the Encyclopedia of the Mouse Genome Encyclopedia, and related software and data. Maintained by Jackson Laboratory, in Bar Harbor, Maine.
NCBI HomoloGene Resource Homology resource which includes both curated and calculated orthologs and homologs for genes represented in UniGene and LocusLink for human, mouse, rat, and zebrafish.
Protocol Online (Your Lab's Reference Book) Provides researchers with collection of links to cell and molecular biology, immunology protocols, along with methods and tips.
Saccharomyces Genome Database Contains the Saccharomyces Genome Database from Stanford University.

ZFIN: The Zebrafish Model Organism Database This link opens in a new window An online database of information for zebrafish researchers, ZFIN serves as the zebrafish model organism database.

Groks Science Radio Show and Podcast Dr. Charles Lee and Dr. Frank Ling host a weekly science program that provides an in-depth look at recent developments in science and technology and examines the effects of these discoveries on our daily lives. Shows are available as podcasts from the Web site and The Internet Archive. Produced at KALX 90.7 FM in Berkeley, CA.
LabDish: A CSHL Newsblog (Cold Spring Harbor Laboratory) Provides readers with engaging and informative coverage of the Cold Spring Harbor Laboratory's scientific research and educational activities and acts as a virtual showcase for interesting events.
Science Podcasts Produced by Science, this weekly podcast offers interesting stories from the journal and its sister sites.
Science Talk - Podcasts Interviews with leading scientists and journalists about current science news. Produced by Scientific American.
SciVee A social community for researchers of all levels that encourages sharing published research through online video presentations. Members can see and hear colleagues describe their research, join specific interest communities, participate in discussions, and create a comprehensive multimedia representation of their own research.
Sounds of Science Podcast from the National Academies Focuses on a wide variety of critical issues in science, technology, and medicine. Provides weekly, 10-minute audio podcasts that describe key findings and important recommendations from the National Academies.
Wikibooks: Health Sciences An open-content textbooks collection that currently includes information on dermatology, emergency medicine, pharmacology, medical imaging, radiation oncology, reproductive health, USMLE Steps 1 and 2, and more.
Wikibooks: Natural Sciences An open-content textbook collection that currently includes information on chemistry, earth sciences, environmental sciences, life sciences, physics, and more.

Bio-protocol A peer-reviewed, open-access collection of high-quality life science protocols covering 10 organisms and 11 research fields. Protocols are accepted by invitation only and are extensively reviewed to ensure experimental reproducibility. Developed by researchers at Stanford University.
Cold Spring Harbor Protocols Interactive online methods database developed by Cold Spring Harbor Laboratory. Includes protocols in cell and molecular biology, genetics, protein science, imaging, and bioinformatics.

Current Protocols This link opens in a new window Includes step-by-step protocols with annotations; alternate and support protocols to accommodate different equipment and desired results; materials lists for each protocol; and more. Access is provided only to full-text content published during the time the Library actively subscribed to each title; as of January 1, 2014, there is no current subscription.

Methods in Enzymology (ScienceDirect) Browse the individual volumes going back to 1955, or search across the collection by title, author, abstract, and keyword. ISSN: 0076-6879.
Publication Date: 1995 - Present

Nature Protocols Publishes secondary research articles that are based on published primary research papers. Covers new techniques and technologies, as well as established methods, used in all fields of the biological, chemical, and clinical sciences. ISSN: 1754-2189; 1750-2799.
Protocol Online (Your Lab's Reference Book) Provides researchers with collection of links to cell and molecular biology, immunology protocols, along with methods and tips.

Journal of Visualized Experiments (JoVE) This link opens in a new window
A peer-reviewed, PubMed-indexed journal devoted to the publication of biological, medical, chemical, and physical research in a video format. Note: The following sections are fully licensed by the UT Southwestern Library: Behavior, Biochemistry, Bioengineering, Biology, Cancer Research, Chemistry, Developmental Biology, Engineering, Environment, Genetics, Immunology & Infection, Medicine, and Neuroscience. Other sections are not licensed, although some content may be available through open access.

BankIt: GenBank Submissions by WWW (NCBI) GenBank submissions on the Web.

BioToolKit This link opens in a new window An annotated directory of links to online molecular biology and neuroinformatics resources, including basic research tools as well as advanced tools enabling integrated, multi-level analysis of the genome, transcriptome, and proteome. Divided into four sections: Nucleic Acid Analysis, Genomics Resources, Protein Structural Imaging and Analysis, and Neuroinformatics.

Ensembl Genome Browser Ensembl provides automatic annotation to human genome data. A central element of the Ensembl project is openness; all data and code are freely available.

FlyBase: A Database of Drosophila Genes & Genomes This link opens in a new window FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. It includes data from the Drosophila Genome Projects and data curated from the literature. FlyBase is a joint project with the Berkeley and European Drosophila Genome Projects.
Gene Structural Annotation: Arabidopsis thaliana Genome This link opens in a new window Provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. In addition, pages on news, information on the Arabidopsis Genome Initiative (AGI), Arabidopsis lab protocols, and useful links are provided.

Genome Statute and Legislation Database (National Human Genome Research Institute) A free, searchable database focusing on genetic information, testing and counseling; insurance and employment discrimination, newborn screening; privacy of genetic information and confidentiality; informed consent; and commercialization and patenting. Contains some full-text legal materials.
Human Genome Project Information Contains basic information about the human genome project including frequently asked questions, contact information, resources, research progress, publications, topical fact sheets, and history. Site sponsored by the DOE Office of Biological and Environmental Research, Human Genome Program.
Human Genome Special Issue (Science) Free, special issue containing the report of the sequencing of the human genome from a group of authors led by Craig Venter of Celera Genomics. Includes other related articles. From Science, v 291, #5507, 16 February 2001.
Microbial Genomes Resources (NCBI) Presents public data from prokaryotic genome sequencing projects. The sequence collection contains data from finished genomes as well as draft assemblies. From the National Center for Biotechnology Information.
National Human Genome Research Institute The mission of the National Human Genome Research Institute is to head the Human Genome Project for the National Institutes of Health (NIH). Refer to Celera Genomics for information involving the private company also involved with the first assembly of the human genome.

NCBI BioProject This link opens in a new window Provides integrated access to nucleotide and protein sequence data in GenBank, EMBL, DDBJ, PIR-International, PRF, Swiss-Prot, and PDB, along with 3D protein structures, genomic mapping information, and PubMed MEDLINE. Contains pre-computed similarity searches for each database record, producing a list of related sequences, structures, and MEDLINE records.

NCBI BLAST Basic Local Alignment Search Tool (BLAST).

NCBI dbEST - Database of Expressed Sequence Tags This link opens in a new window Short (about 300-500 bp) cDNA sequences representing single-pass reads from mRNA. Usually produced in large numbers and represents a snapshot of the genes expressed in a given tissue, and/or at a given developmental stage. Also includes ESTs generated by the Cancer Genome Anatomy Project.
NCBI dbSNP - Database of Single Nucleotide Polymorphisms This link opens in a new window Database serves as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms.

NCBI Gene Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode. Replaces LocusLinks.

NCBI Genome This link opens in a new window Provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups (Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids) and includes complete chromosomes, organelles, and plasmids as well as draft genome assemblies. From the National Center for Biotechnology Information.

NCBI HomoloGene Resource Homology resource which includes both curated and calculated orthologs and homologs for genes represented in UniGene and LocusLink for human, mouse, rat, and zebrafish.
NCBI Human Genome Resources Links to GenBank submission and searching information.

Repbase (Genetic Information Research Institute) This link opens in a new window A database of prototypic sequences representing repetitive DNA from different eukaryotic species, which is being used in genome sequencing projects worldwide as a reference collection for masking and annotation of repetitive DNA (e.g. by RepeatMasker or CENSOR).

UCSC Genome Browser Contains links to the USCS assembly of the current draft of the human genome. This assembly attempts to merge together overlapping fragments, and to order and orient non-overlapping fragments based on mRNA, EST, paired plasmid reads, and other information.