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http://www.nitrc.org/projects/ontology/

Project to discuss, debate, develop and deploy ontological practices for the fMRI community.

Proper citation: Resource Ontology Discussion Group (RRID:SCR_002536) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/iop/depts/neuroimaging/research/imaginganalysis/Software/rBET.aspx

A modified version of the Brain Extraction Tool (BET) that can process rodent brains.

Proper citation: Rodent Brain Extraction Tool (RRID:SCR_002538) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/contrack

An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo.

Proper citation: ConTrack (RRID:SCR_002681) Copy   

•   Source: SciCrunch Registry

http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry

http://www.flymine.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

Proper citation: FlyMine (RRID:SCR_002694) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.charite.de/superpred/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits.

Proper citation: SuperPred: Drug classification and target prediction (RRID:SCR_002691) Copy   

•   Source: SciCrunch Registry

http://rsync.samba.org/

Software that provides rapid incremental file transfer.

Proper citation: rsync (RRID:SCR_003113) Copy   

•   Source: SciCrunch Registry

http://rp-www.cs.usyd.edu.au/~yangpy/software/MFGE.html

A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map.

Proper citation: MF-GE (RRID:SCR_003509) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/charge/

Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra.

Proper citation: Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra (RRID:SCR_004315) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/segtools/

Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.

Proper citation: Segtools (RRID:SCR_004394) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/cpodes

CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules.

Proper citation: CPODES numerical integrator (RRID:SCR_000766) Copy   

•   Source: SciCrunch Registry

http://bamview.sourceforge.net/

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Proper citation: BamView (RRID:SCR_004207) Copy   

•   Source: SciCrunch Registry

http://commonsinabox.org/

A free, distributable, easy-to-install software package of customizable, WordPress-based commons spaces for communities. This software project aimed at turning the infrastructure that successfully powers the CUNY (City University of New York) Academic Commons takes the complexity out of creating a Commons site, helping organizations create a space where their members can discuss issues, collaborate on projects, and share their work. CBOX also provides: * Out-of-the-box functionality with an intuitive set-up that guides site administrators through each step of installation. * A powerful, responsive, highly customizable theme developed for community engagement, based on PressCrew's Infinity Theming Engine. * Responsive design for easy viewing on many devices, including tablets and smartphones. * Collaborative document creation and file sharing. * Reply-By-Email functionality for quick, on-the-go communication. * Compatibility with many other WordPress and BuddyPress themes and plug-ins. * Expansive wiki options. CBOX will be useful to any organization that is looking for a shared space in which to build an engaged community of users and developers. Download their code, peruse their documentation, check out their project demo website, and join their community to find others using CBOX.

Proper citation: Commons In A Box (RRID:SCR_002620) Copy   

•   Source: SciCrunch Registry

http://fascinator.usq.edu.au/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An extensible, open-source platform for managing your digital objects. Using a variety of plugins, you can transform your digital objects into new formats, search and browse through your collection, collaborate through tagging and annotations, and create packages of information for publishing to all manner of systems. Written in Python.

Proper citation: Fascinator (RRID:SCR_001367) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-leipzig.de/Software/RNAplex/

Software tool to rapidly search for short interactions between two long RNAs.

Proper citation: RNAplex (RRID:SCR_002763) Copy   

•   Source: SciCrunch Registry

https://pubmed.ncbi.nlm.nih.gov/21129402/

Source code that allows you to calculate the different measures used in Kreuz T, Chicharro D, Greschner M, Andrzejak RG (2011): Time-resolved and time-scale adaptive measures of spike train synchrony, http://www.sciencedirect.com/science/article/pii/S0165027010006564. Journal of Neuroscience Methods,195, 92-106 & Kreuz T, Chicharro D, Andrzejak RG, Haas JS, and Abarbanel HDI (2009) Measuring multiple spike train synchrony. Journal of Neuroscience Methods 183:287-299 http://www.sciencedirect.com/science/article/pii/S0165027009003616

Proper citation: Time-resolved and time-scale adaptive measures of spike train synchrony (RRID:SCR_001667) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: Visual Molecular Dynamics (RRID:SCR_001820) Copy   

•   Source: SciCrunch Registry

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.80.026217

Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217.

Proper citation: Reliable detection of directional couplings using rank statistics (RRID:SCR_001662) Copy   

•   Source: SciCrunch Registry

https://reich.hms.harvard.edu/software

XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available.

Proper citation: XP-CLR (RRID:SCR_004961) Copy   

•   Source: SciCrunch Registry