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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.
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Proper citation: pyomo (RRID:SCR_024188) Copy
http://sitplus.crea-si.com/index/index.html
Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.
Proper citation: sitplus (RRID:SCR_024344) Copy
https://metacpan.org/dist/AI-FANN
Software Perl wrapper for the Fast Artificial Neural Network library
Proper citation: AI-FANN (RRID:SCR_024060) Copy
https://metacpan.org/dist/Bio-Coordinate
Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
Proper citation: Bio-Coordinate (RRID:SCR_024063) Copy
Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.
Proper citation: Ginkgo CADx (RRID:SCR_024031) Copy
http://samtools.github.io/htsjdk/
Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.
Proper citation: HTSJDK (RRID:SCR_024036) Copy
http://proteomics.ucsd.edu/Software/Inspect/
Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.
Proper citation: InsPecT (RRID:SCR_024038) Copy
https://github.com/klebgenomics/Kaptive
Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.
Proper citation: Kaptive (RRID:SCR_024046) Copy
Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.
Proper citation: JabRef (RRID:SCR_024047) Copy
https://userbase.kde.org/KBibTeX
Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.
Proper citation: KBibTeX (RRID:SCR_024048) Copy
https://github.com/kblin/ncbi-acc-download
Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.
Proper citation: NCBI accession download script (RRID:SCR_024130) Copy
Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.
Proper citation: Lucy (RRID:SCR_024099) Copy
Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.
Proper citation: tacg (RRID:SCR_024374) Copy
https://github.com/tseemann/VelvetOptimiser/
Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.
Proper citation: VelvetOptimiser (RRID:SCR_024376) Copy
Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations.
Proper citation: VisIt (RRID:SCR_024370) Copy
https://desmid.github.io/mview/
Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.
Proper citation: MView (RRID:SCR_024129) Copy
http://rambok.sourceforge.net/
Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.
Proper citation: rambo-k (RRID:SCR_024198) Copy
https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/
Software tool to correct sequencing errors in single pass reads for de novo assembly.
Proper citation: sprai (RRID:SCR_024353) Copy
https://github.com/streamlit/streamlit
Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.
Proper citation: streamlit (RRID:SCR_024354) Copy
https://cme.h-its.org/exelixis/web/software/sweed/
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Proper citation: sweed (RRID:SCR_024357) Copy
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