Background Information
- Genome Glossary (NCBI)Commonly used genome terms with links to associated literature for each term
- Glossary: Human Genome ProjectSome terms commonly used in bioinformatics resources to describe genes, sequence data, protein structures, and sequence similarity (BLAST) searching.
Portals vs Browsers in the world of bioinformatics
- Portal a framework to provide a single point of access to a variety of information and tools
- Browser is used to access information provided by web servers in private networks or files in file systems (like data)
Encyclopedia of Genetics, Genomics, Proteomics, and Informatics by ISBN: 9781402067532Publication Date: 2008Best-selling encyclopedia, covers the basics and the latest in genomics, proteomics, genetic engineering, small RNAs, transcription factories, chromosome territories, stem cells, genetic networks, epigenetics, prions, hereditary diseases, and patents.
Springer Handbook of Bio-/Neuroinformatics by ISBN: 9783642305733Publication Date: 2014The text contains 62 chapters organized in 12 parts, 6 of them covering topics from information science and bioinformatics, and 6 cover topics from information science and neuroinformatics. Each chapter consists of three main sections: introduction to the subject area, presentation of methods and advanced and future developments.
Databases
- Allen Institute for Brain Science1st Database produced: Cell Types Database (profiles individual neurons based on shape, activity...
- Collaborative Research in Computation Neuroscience (CRCN), Data setsHigh-quality experimental data sets that are valuable for testing computational models of the brain and new analysis methods. Data include physiological recordings from sensory and memory systems, as well as eye movement data.
- Genome BrowserCompiled by UC Santa Cruz. Genomes for over 40 organisms
- International Neuroinformatics Coordinating Facility (INCF) DataspaceEnables collaboration between researchers through the sharing of neuroscience data, text, images, sounds, movies, models and simulations. Must create account to access.
- NCBI (National Center for Biotechnology Information)Biomedical and genomic information
- NCBI Biosystems DatabaseAccess to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez.
- Neuroscience Information Framework (NIF)Search multiple individual databases and data sets at once. Results categorized by data type and nervous system level.
- Open fMRIProject dedicated to the free and open sharing of functional magnetic resonance imaging (fMRI) datasets, including raw data.
- OBRC: Online Bioinformatics Resources CollectionUniversity of Pittsburgh; searches annotations and links to over 2400 databases and software
- PDBe: Protein Data Bank in EuropeGeared to the biomedical community. Macromolecular structures and related data; high-quality deposition and annotation facilities for structural data
- PubMed This link opens in a new windowComprehensive medical database of citations to the biomedical literature that includes MEDLINE, in addition to other health databases funded by NIH.
- RCSB Protein Data BankResearch Collaboratory for Structural Bioinformatics. Worldwide repository for information about 3D structures of biological macromolecules. Provides tools for structure visualization.
- UniProtProtein sequences
Portals
- ExPASy: SIB Bioinformatics Resource Portalscientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
- Harvard's Bioinformatics guideSee tabs for Video and Software. Some videos are accessible through YouTube; software may be proprietary but is a list of what's out there
- Freely Available Bioinformatics Services (EMBL-EBI)Includes genes, molecular structures, proteins, software and more.
Protocols
- Protocol ExchangeDiscover and share protocols, join a lab group, comment on protocols, organize your favorites and personalize your experience. Open repository from Nature Publishing Group. Protocols are posted directly by their authors, and are not peer-reviewed or edited.
Analysis, Tools, Workbenches
- BLASTFind regions of similarity between biological sequences.
Atlases
- Allen Brain AtlasData includes the human brain, the mouse brain, and non-human primate
Data Repositories
- Trusted Digital Repository ChecklistAlthough the Center for Research Libraries has only certified a select few, this does not mean that others should be excluded. The criteria provide some guidance to evaluate a repository.
- DataCiteList of repositories
- Recommended RepositoriesList provided by Nature Publishing Group for different science disciplines
- DryadRepository of data underlying peer-reviewed articles in science and medicine
- figsharefigshare allows users to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow.
- GitHubRepository for developers using source code and scripts. Managment for open source and private projects, any type of file. Inteface with ZENODO to obtain your DOI.
- DataONEDataONE will ensure the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data in environmental science. Supported by NSF.
- Data RepositoriesA list of repositories and databases for open data in the sciences and social sciences; part of the Open Access Directory.
- Dataverse NetworkA repository for research data for long term preservation and good archival practices, while researchers can share, keep control of and get recognition for their data.
Community Supprt
Additional Research Guides
Guides from other libraries that may be worth checking:
- Bioinformatics (George Mason University Libraries)See especially tabs for Web Sites and Software Applications
- Bioinformatics Tools (Bates College Library)Covers DNA, RNA, Protein, Genome Viewers, and Sequence Alignment
- Bioinformatics guide: NCBI Information (UNC Charlotte Library)Links for using the NCBI databases: tutorials, YouTube videos
- Bioinformatics guide (University of New Mexico Health Sciences Library)Extensive list of links for NCBI resources as well as under tab for Databases & Web Resources