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http://publications.nigms.nih.gov/multimedia/searchresults.asp?search=All

As part of its multimedia outreach, the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health -- the United States'' medical research agency -- offers audio and video podcasts and other multimedia resources that explore the exciting world of basic biomedical research.

Proper citation: NIGMS Multimedia (RRID:SCR_005712) Copy   

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http://www.topsan.org/

Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation.

Proper citation: TOPSAN (RRID:SCR_005758) Copy   

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http://publications.nigms.nih.gov/chemhealth/

Visit ChemHealthWeb for research highlights, chemist profiles, games and videos and other Web extras. The NIGMS Chemistry of Health booklet describes basic chemistry and biochemistry research that spurs a better understanding of human health.

Proper citation: ChemHealthWeb (RRID:SCR_005851) Copy   

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http://polbase.neb.com/

Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.

Proper citation: Polbase (RRID:SCR_006107) Copy   

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https://phenome.jax.org/centers/QTLA

Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.

Proper citation: QTL Archive (RRID:SCR_006213) Copy   

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http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS

Web service with well defined methods to enable programmatic access to molecular interactions. Standard for computational access to molecular interaction data resources.

Proper citation: PSICQUIC Registry (RRID:SCR_006389) Copy   

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http://www.tcdb.org/

Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run.

Proper citation: Transporter Classification Database (RRID:SCR_004490) Copy   

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http://u-compare.org/

An integrated text mining / natural language processing system based on the Unstructured Information Management Architecture (UIMA) Framework. It allows interoperability of text mining tools and allows the creation of text mining workflows, comparison and visualization of tools. U-Compare can be launched straight from the web or downloaded. As the name implies comparison of components and workflows is a central feature of the system. U-Compare allows sets of components to be run in parallel on the same inputs and then automatically generates statistics for all possible combinations of these components. Once a workflow has been created in U-Compare it can be exported and shared with other users or used with other UIMA compatible tools and so in addition to comparison, U-Compare also functions as a general purpose workflow creation tool. It contains a repository of 50+ biomedical text mining components. These components are included in the U-Compare single-click-to-launch package, ready to use by just drag-and-drop. You can also use this repository independent from the U-Compare system. Link with Taverna It has a link with Taverna for scientific workflows, http://bioinformatics.oxfordjournals.org/content/26/19/2486.abstract, where you can use U-Compare and its workflow from within the Taverna workflow. There are two ways, the U-Compare Taverna plugin and the U-Compare command line mode as a Taverna activity. We have recently integrated it with Peter Murray-Rust''''s OSCAR for Chemistry (see http://www.nactem.ac.uk/cheta/) Web Demo: http://www.nactem.ac.uk/software/cheta/

Proper citation: U-Compare (RRID:SCR_004911) Copy   

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http://www.pantherdb.org/

System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PANTHER (RRID:SCR_004869) Copy   

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http://skatebase.org/

Portal supporting the North East Bioinformatics Collaborative''s project to sequence the genome of the Little Skate. Provided is a clearinghouse for Little Skate Genome Project and other publicly available Skate and Ray (Batoidea) genome data, and tools for data visualization and analysis. Little Skate Genome Project The little skate (Leucoraja erinacea) is a chondrichthyan (cartilaginous) fish native to the east coast of North America. Elasmobranchs (Skates, Rays, and Sharks) exhibit many fundamental vertebrate characteristics, including a neural crest, jaws and teeth, an adaptive immune system, and a pressurized circulatory system. These characteristics have been exploited to promote understanding about human physiology, immunology, stem cell biology, toxicology, neurobiology and regeneration. The development of standardized experimental protocols in elasmobranchs such as L. erinacea and the spiny dogfish shark (Squalus acanthias) has further positioned these organisms as important biomedical and developmental models. Despite this distinction, the only reported chondrichthyan genome is the low coverage (1.4x) draft genome of the elephant shark (Callorhinchus milii). To close the evolutionary gaps in available elasmobranch genome sequence data, and generate critical genomic resources for future biomedical study, the genome of L. erinacea is being sequenced by the North East Bioinformatics Collaborative (NEBC). As close evolutionary relatives, the little skate sequence will facilitate studies that employ dogfish shark and other elasmobranchs as model organisms. Skate tools include the SkateBLAST and the Skate Genome Browsers: Little Skate Mitochondrion, Thorny Skate Mitochondrion, and Ocellate Spot Skate Mitochondrion.

Proper citation: SkateBase (RRID:SCR_005302) Copy   

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https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

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http://bioportal.bioontology.org/

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Proper citation: BioPortal (RRID:SCR_002713) Copy   

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https://simtk.org/home/foldvillin

An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations.

Proper citation: Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) Copy   

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http://pir.georgetown.edu/pro/

An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).

Proper citation: PRO (RRID:SCR_002902) Copy   

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http://cytoscape.org

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Proper citation: Cytoscape (RRID:SCR_003032) Copy   

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http://www.bioperl.org

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BioPerl (RRID:SCR_002989) Copy   

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http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

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http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/

A database of S. cerevisiae H/ACA and C/D box snoRNAs, useful for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. The tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.

Proper citation: Yeast snoRNA Database (RRID:SCR_007980) Copy   

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http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal

Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function.

Proper citation: Jackal (RRID:SCR_008665) Copy   

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https://simtk.org/home/lapack

This project is the SimTK Core implementation of the extremely reliable, high speed linear algebra package LAPACK and the underlying BLAS library on which LAPACK is built. It uses ATLAS to generate hand tuned BLAS kernels for a variety of hardware platforms, including multiprocessors, using a variety of operating systems including Windows, Mac, and Red Hat Linux. These platforms are pre-built and make the binaries available as a single shared library which can be conveniently used by any program. This means that users who are not experts in high performance scientific computation can nonetheless use the fastest linear algebra methods available for their machines.

Proper citation: LAPACK linear algebra library (RRID:SCR_008661) Copy   

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