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http://www.imb.sinica.edu.tw/core/publicfacilities/pdf/LAS-1000plus_om_e_ver2.pdf
A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned.
Proper citation: Image Reader LAS-1000 (RRID:SCR_014585) Copy
https://www.edaq.com/ES280_PowerChrom-Software
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. A software which collects, displays, and analyzes chromatographic signals. This software doesn't require any programming, and collects signals from one or two detectors. PowerChrom is supplied as part of the PowerChrom system, or separately for use with e-corder recording systems.
Proper citation: PowerChrom (RRID:SCR_014588) Copy
http://www.cbcb.umd.edu/software/metapath
A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG.
Proper citation: Metapath (RRID:SCR_014621) Copy
A programming library that uses standard graphics cards to produce 2D and 3D visual stimuli for vision research experiments.
Proper citation: Vision Egg (RRID:SCR_014589) Copy
A public–private initiative that supports research that provides evidence on the biological validity of therapeutic targets and that gain insight into the effectiveness of pharmacological intervention. It aims to provide a research and development framework that applies human disease. It shares its information openly.
Proper citation: Open Targets (RRID:SCR_014622) Copy
http://sea.rice.edu/sites/g/files/bxs231/f/Using%20the%20Axioskop%20Details%20Guide%20061413_0.pdf
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 19, 2022. Software used to control the Zeiss Axioskop microscope.
Proper citation: Zeiss Axioskop Software (RRID:SCR_014587) Copy
http://huttenhower.sph.harvard.edu/humann
A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities.
Proper citation: HUMAnN (RRID:SCR_014620) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub.
Proper citation: HDD Access (RRID:SCR_014581) Copy
http://www.proteinsimple.com/fluorchem_q.html
A software used for quantitative Western blot imaging and analysis. This software is compatible with several dyes and kits, providing extra flexibility for application. This software is designed to be able to look at multiple proteins simultaneously on a single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated isoforms.
Proper citation: FluorChem Q Imager (RRID:SCR_014549) Copy
Ratings or validation data are available for this resource
http://www.olympus-lifescience.com/en/software/cellsens/
Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.
Proper citation: Olympus cellSens Software (RRID:SCR_014551) Copy
A non-profit organization that awards grants to a broad spectrum of charities, including those that benefit spinal cord injury efforts. The Foundation is primarily dedicated to funding extensive research, education and quality of life programs for improving the lives of people affected by spinal cord injury.
Proper citation: CRAIG H. NEILSEN FOUNDATION (RRID:SCR_014552) Copy
Elixir Interoperability Platform to help people and machines to discover, access, integrate and analyse biological data. Encourages life science community to adopt standardized file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. Bioinformatics resource registry that provides scientific and technical information about analytical tools and data services for bioinformatics. Gateway to databases and tools for life science data analysis.Provides comprehensive and up-to-date catalogue of resources that are interactive and downloadable, and that offer programmatic access. The registry also allows the community to upload their own resources to the registry following a simple log in procedure.
Proper citation: ELIXIR Tools and Data Services Registry (RRID:SCR_014556) Copy
http://www.brainandspinalinjury.org
A center that conducts basic science and clinical research concerning spinal cord injury located at both the University of California San Francisco and the Zuckerberg San Francisco General Hospital.
Proper citation: UCSF Brain and Spinal Injury Center (UCSF-BASIC) (RRID:SCR_014553) Copy
https://github.com/galaxyproject/bioblend
A Python library which provides Python access to and interaction with Galaxy's API and CloudMan. The library allows users to create a CloudMan compute cluster via an API and directly from a local machine, reconnect to an existing CloudMan instance and manipulate it, and interact with Galaxy via a straightforward API and an object-oriented API. The library itself can be used with either service irrespective of the other.
Proper citation: BioBlend Library (RRID:SCR_014557) Copy
http://krasnow1.gmu.edu/CENlab/software.html
Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.
Proper citation: NeuroRD (RRID:SCR_014769) Copy
https://www.comsol.com/comsol-multiphysics
General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating.
Proper citation: COMSOL Multiphysics (RRID:SCR_014767) Copy
http://www.ccdc.cam.ac.uk/free_services/relibase_free
Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.
Proper citation: Relibase (RRID:SCR_014888) Copy
http://enigma.ini.usc.edu/protocols/dti-protocols/
Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols.
Proper citation: ENIGMA-DTI Pipeline (RRID:SCR_014649) Copy
https://github.com/HussainiLab/BatchTINTV3
GUI created by the Taub Institute in order to create an end-user friendly batch processing solution to complement Axona's new command line modification of TINT. This GUI allows the user to define a directory. Within this directory it will be continuously (unless closed) searching for new files to analyze via TINT.
Proper citation: BatchTINT (RRID:SCR_014804) Copy
http://cbdm.uni-mainz.de/hippie/
Web tool used to generate confidence scored and functionally annotated human protein-protein interaction networks. Users can run a protein query using a UniProt identifier (ID or accession), gene symbol or Entrez gene id, or a network query using set fields.
Proper citation: HIPPIE (RRID:SCR_014651) Copy
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