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http://shendurelab.github.io/MIPGEN/

Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline.

Proper citation: MIPgen (RRID:SCR_003325) Copy   

•   Source: SciCrunch Registry

http://neuroscience.med.cornell.edu/

The Weill Medical College of Cornell University has a long tradition of neuroscience research. The faculty is large, and the research programs tackle the fundamental questions in the field at all levels - from genes to cells to systems to behavior. The neuroscience community at Weill Cornell spans two campuses. The main one, containing the medical school and associated hospitals, is located on the upper east side of Manhattan, adjacent to Rockefeller University and across the street from the Memorial Sloan-Kettering Cancer Center. The second campus, with the rapidly growing Burke-Cornell Research Institute, is located in White Plains. The following graduate programs are offered: Neuroscience PhD, Tri-Institutional MD-PhD, Physiology and Biophysics, and Tri-Institutional Graduate program in Computational Biology and Medicine.

Proper citation: Cornell University Neuroscience (RRID:SCR_003324) Copy   

•   Source: SciCrunch Registry

https://www.msu.edu/~brains/index.html

The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. Atlases and brain sections are available for a variety of mammals, and we are also developing a series of labeled atlases of stained sections for educators, students, and researchers. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan. What we are doing currently at Michigan State is a series of demonstration projects for publicizing the contents of the collections and ways in which they can be used. For example, the images from the collection can be used for comparative brain study. We have prepared databases of the contents of the collections for presentation and use on this site, as well as for downloading by users in several formats. We are also developing a series of labeled atlases of stained sections for educators, students, and researchers. This internet site is associated with the Comparative Mammalian Brain Collections site. All of the images are in JPEG or GIF format.

Proper citation: Michigan State University Brain Biodiversity Bank (RRID:SCR_003289) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/popoolation2/

Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PoPoolation2 (RRID:SCR_003284) Copy   

•   Source: SciCrunch Registry

http://www.yaleruddcenter.org/

A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma.

Proper citation: Yale Rudd Center for Food Policy and Obesity (RRID:SCR_003283) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/FB-CV

A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.

Proper citation: FlyBase Controlled Vocabulary (RRID:SCR_003318) Copy   

•   Source: SciCrunch Registry

http://www.brainbank.mclean.org/

Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens.

Proper citation: Harvard Brain Tissue Resource Center (RRID:SCR_003316) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/FYPO

A formal ontology of phenotypes observed in fission yeast that is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.

Proper citation: Fission Yeast Phenotype Ontology (RRID:SCR_003315) Copy   

•   Source: SciCrunch Registry

https://github.com/outbig/DAFGA

A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur.

Proper citation: DAFGA (RRID:SCR_003319) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/johanneskoester/snakemake/wiki/

A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.

Proper citation: Snakemake (RRID:SCR_003475) Copy   

•   Source: SciCrunch Registry

http://bbid.irp.nia.nih.gov/

Database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. The rationale for this collection is that: # Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. # Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. # The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. # Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. # All images are attributable to the original authors. All pathways or other biological systems described are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. Image/pathway submissions are welcome.

Proper citation: Biological Biochemical Image Database (RRID:SCR_003474) Copy   

•   Source: SciCrunch Registry

http://knowledgemap.mc.vanderbilt.edu/research/content/phewas-r-package

Software package contains methods for performing Phenome-Wide Association Study.

Proper citation: PheWAS R Package (RRID:SCR_003512) Copy   

•   Source: SciCrunch Registry

https://github.com/BauerLab/ngsane

Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

Proper citation: NGSANE (RRID:SCR_003478) Copy   

•   Source: SciCrunch Registry

http://sbgrid.org/

Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application.

Proper citation: Structural Biology Grid (RRID:SCR_003511) Copy   

•   Source: SciCrunch Registry

http://www.cellimagelibrary.org/

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

Proper citation: Cell Image Library (CIL) (RRID:SCR_003510) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/snape-pooled/

Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

Proper citation: SNAPE-pooled (RRID:SCR_003476) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/bpipe/

Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Proper citation: Bpipe (RRID:SCR_003471) Copy   

•   Source: SciCrunch Registry

http://www.lgm.upmc.fr/parseq/

Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.

Proper citation: Parseq (RRID:SCR_003464) Copy   

•   Source: SciCrunch Registry

http://solstice.eplt.washington.edu/

A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development.

Proper citation: Solstice (RRID:SCR_003463) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/popcomm-ontology/

An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO).

Proper citation: Population and Community Ontology (RRID:SCR_003462) Copy   

•   Source: SciCrunch Registry