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http://sourceforge.net/projects/splicegrapher/

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

Proper citation: SpliceGrapher (RRID:SCR_006657) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bycom/

A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output.

Proper citation: Bycom (RRID:SCR_000659) Copy   

•   Source: SciCrunch Registry

http://bamview.sourceforge.net/

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Proper citation: BamView (RRID:SCR_004207) Copy   

•   Source: SciCrunch Registry

http://owlapi.sourceforge.net/

The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: OWL API (RRID:SCR_005734) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry

http://neurofitter.sourceforge.net

Neurofitter is software for parameter tuning of electrophysiological neuron models. It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc.

Proper citation: Neurofitter (RRID:SCR_005843) Copy   

•   Source: SciCrunch Registry

http://orchem.sourceforge.net

OrChem is an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today''s powerful database servers to provide fast response times in equally large data sets. OrChem is an Oracle chemistry plug-in using the Chemistry Development Kit (CDK). The CDK is an open source Java library for Chemoinformatics and Bioinformatics. OrChem is maintained by the chemoinformatics and metabolism team of the European Bioinformatics Institute. Oracle Data cartridges extend the capabilities of the Oracle server. For chemistry various commercial cartridges exist that facilitate searching and analyzing chemical data. OrChem also provides functionality like this, but is not a cartridge. It doesn''t need Oracle''s extensibility architecture because its Java components run as Java stored procedures inside the Oracle standard JVM (Aurora). OrChem is suitable for Oracle 11G and onwards. Starting with Oracle 11g release 1 (11.1) there is a just-in-time(JIT) compiler for Oracle JVM environment. A JIT compiler for Oracle JVM enables much faster execution because it manages the invalidation, recompilation, and storage of code without an external mechanism. This new Oracle feature makes Java classes perform better than before.

Proper citation: OrChem (RRID:SCR_008865) Copy   

•   Source: SciCrunch Registry

http://andestools.sourceforge.net/

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Proper citation: ANDES (RRID:SCR_002791) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) 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://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

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

http://uc-echo.sourceforge.net/

Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.

Proper citation: ECHO (RRID:SCR_011851) Copy   

•   Source: SciCrunch Registry

http://tagcleaner.sourceforge.net/

A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.

Proper citation: TagCleaner (RRID:SCR_011846) Copy   

•   Source: SciCrunch Registry

http://rnaseq-mats.sourceforge.net/

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy   

•   Source: SciCrunch Registry

http://nipy.org

Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.

Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/cdao/

A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science

Proper citation: Comparative Data Analysis Ontology (RRID:SCR_010297) Copy   

•   Source: SciCrunch Registry

http://bio-bwa.sourceforge.net/

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

Proper citation: BWA (RRID:SCR_010910) Copy   

•   Source: SciCrunch Registry