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http://staden.sourceforge.net/

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Proper citation: Staden Package (RRID:SCR_005629) Copy   

•   Source: SciCrunch Registry

http://snp-magma.sourceforge.net

Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem.

Proper citation: MAGMA (RRID:SCR_005757) Copy   

•   Source: SciCrunch Registry

http://brainnetworks.sourceforge.net

Brain Networks: Code to perform network analysis on brain imaging data.

Proper citation: Brain Networks (RRID:SCR_005841) Copy   

•   Source: SciCrunch Registry

http://estscan.sourceforge.net/

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics.

Proper citation: ESTScan (RRID:SCR_005742) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bless-ec/

Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory.

Proper citation: BLESS (RRID:SCR_005963) Copy   

•   Source: SciCrunch Registry

https://compbio.dfci.harvard.edu/predictivenetworks//

A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.

Proper citation: Predictive Networks (RRID:SCR_006110) Copy   

•   Source: SciCrunch Registry

http://rdock.sourceforge.net/

A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.

Proper citation: rDock (RRID:SCR_002838) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fas-dpd/

Software program to design degenerate primers for PCR.

Proper citation: FAS-DPD (RRID:SCR_003068) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/salt1/

Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.

Proper citation: SALT (RRID:SCR_003187) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/xorro-overlap/

Efficient paired-read overlap software program for use with Illumina sequencing.

Proper citation: XORRO (RRID:SCR_003181) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.sfu.ca/software-novelseq

Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

Proper citation: NovelSeq (RRID:SCR_003136) Copy   

•   Source: SciCrunch Registry

http://mrcanavar.sourceforge.net/

Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

Proper citation: mrCaNaVaR (RRID:SCR_003135) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/primerdesigner/

High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.

Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/saskprimerfs/

Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.

Proper citation: SaskPrimerFS (RRID:SCR_003159) Copy   

•   Source: SciCrunch Registry

http://niftilib.sourceforge.net

Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library.

Proper citation: Niftilib (RRID:SCR_003355) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MMO

An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.

Proper citation: Measurement Method Ontology (RRID:SCR_003373) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dranew/defuse

Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.

Proper citation: deFuse (RRID:SCR_003279) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CMO

An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.

Proper citation: Clinical Measurement Ontology (RRID:SCR_003291) Copy   

•   Source: SciCrunch Registry

http://primerseq.sourceforge.net/

Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.

Proper citation: PrimerSeq (RRID:SCR_003295) Copy   

•   Source: SciCrunch Registry

http://www.mindtouch.com/

A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more.

Proper citation: Mindtouch DekiWiki (RRID:SCR_003425) Copy   

•   Source: SciCrunch Registry