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http://sourceforge.net/projects/gemi/

Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.

Proper citation: Gemi (RRID:SCR_003211) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vtontology/

A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.

Proper citation: Vertebrate Trait Ontology (RRID:SCR_003214) Copy   

•   Source: SciCrunch Registry

http://geoss.sourceforge.net/

A complete software system used to store and analyze gene expression data.

Proper citation: GEOSS (RRID:SCR_003401) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/NEMO/?p=summary

Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).

Proper citation: NEMO Ontology (RRID:SCR_003386) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/amplicon/

Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

Proper citation: Amplicon (RRID:SCR_003294) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/FB-SP

The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

Proper citation: Fly Taxonomy (RRID:SCR_003317) Copy   

•   Source: SciCrunch Registry

http://theswo.sourceforge.net

An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

Proper citation: Software Ontology (RRID:SCR_003493) Copy   

•   Source: SciCrunch Registry

http://libeep.sourceforge.net/

Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.

Proper citation: LIBEEP (RRID:SCR_009591) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/w2mhs/

An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis.

Proper citation: Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) Copy   

•   Source: SciCrunch Registry

http://cliiq.sourceforge.net/Home

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

Proper citation: CLIIQ (RRID:SCR_009972) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://moose.sourceforge.net/

MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty. Sponsors: - National Center of Biological Sciences (NCBS) - National Institutes of Health (NIH) Collaboration - EU-India grid - Department of Atomic Energy Science Research Council (DAE/SRC) - Department of Biotechnology (DBT)

Proper citation: Multiscale Object Orientation Simulation Environment (RRID:SCR_008031) Copy   

•   Source: SciCrunch Registry

http://ebardenovo.sourceforge.net/

Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Proper citation: EBARDenovo (RRID:SCR_011890) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene

An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.

Proper citation: SeqGene (RRID:SCR_011861) Copy   

•   Source: SciCrunch Registry

http://bayescall.sourceforge.net/

An efficient model-based base-calling algorithm for high-throughput sequencing.

Proper citation: naiveBayesCall (RRID:SCR_011866) Copy   

•   Source: SciCrunch Registry

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mtoolbox/

Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.

Proper citation: MToolBox (RRID:SCR_012112) Copy   

•   Source: SciCrunch Registry

http://revister.sourceforge.net/

Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci.

Proper citation: ReviSTER (RRID:SCR_012113) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virtools/

Software for a low frequency Virus Variant detection pipeline for Illumina data.

Proper citation: VirVarSeq (RRID:SCR_012116) Copy   

•   Source: SciCrunch Registry