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Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.
Proper citation: neurodebian (RRID:SCR_004401) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
http://pfind.ict.ac.cn/se/plink/
Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: pFind Studio: pLink (RRID:SCR_000084) Copy
https://code.google.com/p/guardd/
MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.
Proper citation: GUARDD (RRID:SCR_000040) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
https://code.google.com/p/knime4bio/
A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills.
Proper citation: Knime4Bio (RRID:SCR_005376) Copy
https://code.google.com/p/phenoman/
An interactive software program that integrates phenotypic data exploration, selection, management and quality control using a unified platform for association studies of rare and common variants.
Proper citation: PhenoMan (RRID:SCR_005249) Copy
http://statgenpro.psychiatry.hku.hk/limx/kggseq/
A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.
Proper citation: KGGSeq (RRID:SCR_005311) Copy
http://www.broadinstitute.org/software/scripture/
Software for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.
Proper citation: Scripture (RRID:SCR_005269) Copy
http://info.gersteinlab.org/PeakSeq
A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.
Proper citation: PeakSeq (RRID:SCR_005349) Copy
http://www.bioinf.uni-leipzig.de/Software/segemehl/
A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.
Proper citation: Segemehl (RRID:SCR_005494) Copy
http://pass.cribi.unipd.it/cgi-bin/pass.pl
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PASS (RRID:SCR_005490) Copy
A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.
Proper citation: Maq (RRID:SCR_005485) Copy
http://code.google.com/p/mosaik-aligner/
A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope.
Proper citation: MOSAIK (RRID:SCR_005486) Copy
http://code.google.com/p/ea-utils/
Command-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
Proper citation: ea-utils (RRID:SCR_005553) Copy
http://bioinfo2.ugr.es/MethylExtract/
A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.
Proper citation: MethylExtract (RRID:SCR_005446) Copy
http://campagnelab.org/software/gobyweb/
Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.
Proper citation: GobyWeb (RRID:SCR_005443) Copy
http://sourceforge.net/p/treq/home/Home/
A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.
Proper citation: TreQ (RRID:SCR_005505) Copy
http://diprogb.fli-leibniz.de/
Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand.
Proper citation: DiProGB (RRID:SCR_005651) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
