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Web based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform.
Proper citation: SourceForge (RRID:SCR_004365) Copy
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
https://sourceforge.net/projects/bva-io/
Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.
Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy
A complete software system used to store and analyze gene expression data.
Proper citation: GEOSS (RRID:SCR_003401) Copy
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
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
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
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
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) Copy
An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.
Proper citation: Jmol (RRID:SCR_003796) Copy
http://rubioseq.sourceforge.net/
Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.
Proper citation: RUbioSeq (RRID:SCR_002508) Copy
http://sourceforge.net/projects/b-o-s-s/
Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.
Proper citation: Batch Oligo Selection Script (RRID:SCR_002808) Copy
http://sourceforge.net/projects/mipe/
A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.
Proper citation: MIPE (RRID:SCR_003065) Copy
Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.
Proper citation: SobekCM (RRID:SCR_003225) Copy
http://mrsfast.sourceforge.net/
A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)
Proper citation: mrsFAST (RRID:SCR_003128) Copy
http://www.metabolomics-msi.org
Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations.
Proper citation: Metabolomics Standards Initiative (RRID:SCR_003246) Copy
http://splicq.sourceforge.net/
A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.
Proper citation: SpliCQ (RRID:SCR_003266) Copy
http://sourceforge.net/projects/orfer/
An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.
Proper citation: ORFprimer (RRID:SCR_003269) Copy
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
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
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