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https://github.com/

A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.

Proper citation: GitHub (RRID:SCR_002630) Copy   

•   Source: SciCrunch Registry

http://www.isi.edu/integration/karma/

An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database.

Proper citation: Karma (RRID:SCR_003732) Copy   

•   Source: SciCrunch Registry

http://impactstory.org/

A web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.

Proper citation: ImpactStory (RRID:SCR_002632) Copy   

•   Source: SciCrunch Registry

https://github.com/NeuroimagingMetaAnalysis/ibma

Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's.

Proper citation: IBMA toolbox (RRID:SCR_003772) Copy   

•   Source: SciCrunch Registry

https://github.com/scidash/sciunit

A test-driven framework for formally validating scientific models against data.

Proper citation: SciUnit (RRID:SCR_014528) Copy   

•   Source: SciCrunch Registry

http://bd2k.ini.usc.edu/tools/bdbag/

Software package with tools which assemble, identify, and provide access to subsets of data in a large and complex data collection workflow. The software utilities work primarily with BagIt packages that conform the BDDS Bagit and BDDS Bagit/RO profiles. JSON-LD is used to provide a standard way for linking metadata with existing ontologies and vocabularies.

Proper citation: Big Data Bag (RRID:SCR_014624) Copy   

•   Source: SciCrunch Registry

http://omop.org/

Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues

Proper citation: Observational Medical Outcomes Partnership (RRID:SCR_003724) Copy   

•   Source: SciCrunch Registry

http://force11.org/

A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.

Proper citation: FORCE11 (RRID:SCR_005334) Copy   

•   Source: SciCrunch Registry

https://github.com/StateSpaceModels

An open source library built to reduce technical friction and help modelers share their work. Models within SSM can be used for inference of time-series analysis.

Proper citation: State Space Models (RRID:SCR_014647) Copy   

•   Source: SciCrunch Registry

https://github.com/NeuroBox3D/AnaMorph

Framework for creating 3D neuronal morphologies from point/diameter descriptions.

Proper citation: AnaMorph (RRID:SCR_015012) Copy   

•   Source: SciCrunch Registry

https://library.ucsd.edu/research-and-collections/digital-collections/dams.html

A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace.

Proper citation: Digital Asset Management System (RRID:SCR_000491) Copy   

•   Source: SciCrunch Registry

http://aebruno.github.io/fusim/

A software tool for simulating fusion transcripts from a reference genome.

Proper citation: FUSIM (RRID:SCR_001015) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSCut

A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

Proper citation: BRAINSCut (RRID:SCR_000861) Copy   

•   Source: SciCrunch Registry

http://www.openworm.org/

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

Proper citation: OpenWorm (RRID:SCR_014650) Copy   

•   Source: SciCrunch Registry

https://github.com/Yandell-Lab/taxonomer_0.5

Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to.

Proper citation: Taxonomer (RRID:SCR_014655) Copy   

•   Source: SciCrunch Registry

https://github.com/ebi-uniprot/ProtVista#annotations:r3_M7HqlEea7DSd1-qZqyw

A BioJS viewer for protein sequence features.

Proper citation: ProtVista (RRID:SCR_014623) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry

http://stanfordnlp.github.io/CoreNLP/

A Java suite of core natural language analysis tools. It can take raw human language text input and give multiple outputs, including the base forms of words, their parts of speech, and marked up structure of sentences in terms of phrases or word dependencies. Supported languages include English, Arabic, Chinese, French, German, and Spanish.

Proper citation: Stanford CoreNLP (RRID:SCR_014778) Copy   

•   Source: SciCrunch Registry

http://microdraw.pasteur.fr/

Web application used to visualise and annotate collaboratively high resolution histology data. In short, it uses public ontologies to create collaborative, community-curated atlases. Annotations are vectorial, and users can use boolean operations to combine, subtract and split regions.

Proper citation: MicroDraw (RRID:SCR_014748) Copy   

•   Source: SciCrunch Registry

https://github.com/SantamariaLab/NeuroManager

Simulation submission manager for computational neuroscience. It manages simulation processing, file transfers, and job submission for a heterogeneous mixture of standalone server, cluster, and cloud servers.

Proper citation: NeuroManager (RRID:SCR_015559) Copy   

•   Source: SciCrunch Registry