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http://sourceforge.net/projects/phosphosite/

A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.

Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) 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://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://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://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://sourceforge.net/apps/mediawiki/mummergpu/index.php?title=MUMmerGPU

Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.

Proper citation: MUMmerGPU (RRID:SCR_001200) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/skewer/

Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.

Proper citation: skewer (RRID:SCR_001151) Copy   

•   Source: SciCrunch Registry

http://iso2mesh.sourceforge.net/

A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling.

Proper citation: iso2mesh (RRID:SCR_013202) Copy   

•   Source: SciCrunch Registry

http://perlprimer.sourceforge.net/

A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.

Proper citation: PerlPrimer (RRID:SCR_012038) Copy   

•   Source: SciCrunch Registry

https://mzmatch.sourceforge.net/MetAssign.php

Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.

Proper citation: MetAssign (RRID:SCR_000092) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-cleaner/

Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.

Proper citation: NGS-Cleaner (RRID:SCR_000574) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/olorin

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

Proper citation: OLORIN (RRID:SCR_002015) Copy   

•   Source: SciCrunch Registry

http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

•   Source: SciCrunch Registry

http://od1n.sourceforge.net

A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

Proper citation: Object-Oriented Development Interface for NMR (RRID:SCR_005974) Copy   

•   Source: SciCrunch Registry

http://mcx.sf.net/mmc/

A Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores.

Proper citation: Mesh-based Monte Carlo (MMC) (RRID:SCR_006950) Copy   

•   Source: SciCrunch Registry

http://biomail.sourceforge.net/biomail/

BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database. BioMail is free and will stay free. What does BioMail do? Periodically BioMail does a user-customized Medline search and sends all matching articles recently added to Medline to the users'' e-mail address. HTML-formatted e-mails generated by BioMail can be used to view selected references in medline format (compatible with most reference manager programs). Why is BioMail helpful? If you use Medline, it may be hard to remember when you did your last search. Often you must scan titles you have already seen to be certain you didn''t miss an important reference. BioMail will perform routine searches for you. This program alerts users to all new papers in their fields automatically. It also helps the user to ''refine'' search patterns once and for all. There is no need to wonder: ''What was that great search pattern I used last Saturday?''. All patterns are safe in the database and can be accessed, tuned, or deleted any time. It is also useful for countries where access to the Internet is not yet widely available. If a person has a permanent e-mail address, but only sporadic www access, she/he only needs to fill out a BioMail form once and then will receive new references from Medline continually.

Proper citation: BioMail (RRID:SCR_008174) 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