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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977.
Proper citation: Stanford Research Institute International (RRID:SCR_004926) Copy
http://neuralensemble.org/neo/
A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.
Proper citation: Neo (RRID:SCR_000634) Copy
http://www.helsinki.fi/bsg/software/BEBaC/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.
Proper citation: BEBaC (RRID:SCR_000621) Copy
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco
Proper citation: CryptoBase (RRID:SCR_000780) Copy
https://code.google.com/p/glycoworkbench/
A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.
Proper citation: GlycoWorkbench (RRID:SCR_000782) Copy
Company focused on animal welfare and pest prevention in the wool industry.
Proper citation: Australian Wool Innovation Limited (RRID:SCR_000775) Copy
Discontinued
https://github.com/PacificBiosciences/blasr
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BLASR (RRID:SCR_000764) Copy
http://sourceforge.net/projects/gmcloser/
Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.
Proper citation: GMcloser (RRID:SCR_000646) Copy
http://sourceforge.net/projects/detecttd/
Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.
Proper citation: detecttd (RRID:SCR_000681) Copy
http://sourceforge.net/projects/fastuniq/
A software tool for removal of de novo duplicates in paired short DNA sequences.
Proper citation: FastUniq (RRID:SCR_000682) Copy
https://www.thermofisher.com/order/catalog/product/4474950
A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.
Proper citation: Sequencing Analysis Software (RRID:SCR_000718) Copy
http://psychiatry.stanford.edu/
A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine.
Proper citation: Stanford University Psychiatry and Behavioral Sciences (RRID:SCR_000719) Copy
http://www.scrippscollege.edu/academics/department/neuroscience/index.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that prepares the student for graduate work in biology, psychology, neuroscience, or preparation for medical school or a career in the health services.
Proper citation: Scripps Women's College, Neuroscience Department (RRID:SCR_000717) Copy
https://github.com/shinout/clipcrop
Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.
Proper citation: clipcrop (RRID:SCR_000678) Copy
A non-profit charity dedicated to providing education about animal research for the purpose of protecting medical and scientific progress. The organization seeks to provide accurate and incisive information to foster a balanced public debate on animal research issues. They work to do outreach by distributing timely and relevant news, information and analysis about animal rights extremism to the research community.
Proper citation: Americans for Medical Progress (RRID:SCR_000711) Copy
http://sourceforge.net/projects/triagetools/
A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.
Proper citation: TriageTools (RRID:SCR_000675) Copy
http://pharmacy.oregonstate.edu/
The college of pharmacy at Oregon State University that offers professional education in pharmacy. The foundational goals are to provide professional education, foster research to contribute to public health initiatives and promote safe and affordable medication access.
Proper citation: Oregon State University College of Pharmacy (RRID:SCR_000715) Copy
http://software.markdpreston.com/varb
A variation browsing and analysis tool for variants derived from next-generation sequencing data.
Proper citation: VarB (RRID:SCR_000671) Copy
A graduate program for pharmacology and toxicology that is a component of the Virginia Commonwealth University. This organization also performs studies on medical disorders, and new pharmacology agents and their effects on human health.
Proper citation: Virginia Commonwealth University, Department of Pharmacology (RRID:SCR_000666) Copy
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