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https://www.bcforms.org

Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.

Proper citation: BcForms (RRID:SCR_018654) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://www.datanator.info

Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.

Proper citation: Datanator (RRID:SCR_018651) Copy   

•   Source: SciCrunch Registry

https://github.com/KarrLab/de_sim

Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models.

Proper citation: DE-Sim (RRID:SCR_018770) Copy   

•   Source: SciCrunch Registry

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/

Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.

Proper citation: RiboTaper (RRID:SCR_018880) Copy   

•   Source: SciCrunch Registry

https://proxl-ms.org/

Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.

Proper citation: Protein Cross-Linking Database (RRID:SCR_021027) Copy   

•   Source: SciCrunch Registry

http://www.kojak-ms.org/

Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets.

Proper citation: Kojak (RRID:SCR_021028) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/FLASH/

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

Proper citation: FLASH (RRID:SCR_005531) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ncmi.bcm.edu/ncmi/

Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods.

Proper citation: National Center for Macromolecular Imaging (RRID:SCR_001445) Copy   

•   Source: SciCrunch Registry

http://www.macchess.cornell.edu/

MacCHESS Synchrotron Source for Structural Biology advances structural characterization of proteins and biomolecules critical for understanding key biological processes and properties through leveraging both established and emerging X-ray synchrotron technologies. Used to collect data that comprises all or part of research programs.

Proper citation: MacCHESS (RRID:SCR_001443) Copy   

•   Source: SciCrunch Registry

http://panomics.pnnl.gov/

Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use.

Proper citation: Proteomics Research Center for Integrative Biology (RRID:SCR_001098) Copy   

•   Source: SciCrunch Registry