Search Results for "c-sharp" - Page 12
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Showing 938 open source projects for "c-sharp"
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Visual Blast
GUI to accelerate protein and nucleotide BLAST analysis
BLAST (Basic Local Alignment Search Tool) is a popular program that retrieves a library of sequences that resemble the query. The major problem experienced by new users of BLAST revolves around constructing syntactically and semantically correct command line, getting input files into acceptable formats and assessing the output. Visual BLAST is a Graphical User Interface written in C# and it was developed to simplify the parameters setting for BLAST searches. Visual BLAST aims to make BLAST... -
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GenoEye
a genome visualization library
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MSL
http://dx.doi.org/10.1002/jcc.22968
MSL is a C++ library that enables the computational study of macromolecules. The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own molecular modeling methods. Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein... -
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ESTReMo
An evolutionary simulator of transcription regulatory networks
ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds. -
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Dynamis
Simple ODE solver for dynamical systems
Dynamis is a simple ODE solver implemented in C for studying dynamical systems (e.g. population biology). -
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A simple database designed to allow easy storage and retrieval of Biosort data for C. elegans, but which has a wide potential application for organizing large datasets.
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CQRlib is an ANSI C implementation of a utility library for quaternion arithmetic and quaternion rotation math.
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smalt
A mapper for DNA sequencing reads
SMALT aligns DNA sequencing reads with genomic reference sequences. It employs hashing combined with dynamic programming. -
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QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Contains mrFAST and mrsFAST. Joint development by University of Washington and Simon Fraser University
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ExonFinder
A pipeline to extract novel cassette exons/retained-introns
ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat. -
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Ezys
Ezys 3D medical image registration program
Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a... -
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the... -
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BiomeNet
BAYESIAN INFERENCE OF METABOLIC DIVERGENCE AMONG MICROBIAL COMMUNITIES
Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic networks among microbial communities. To infer the structure of community-level metabolic... -
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GUDM
A tool for pre-processing and fusing heterogeneous datasets
Global Unified Data Modeler (GUDM) is a bioinformatics software tool used for pre-processing and integrating multiple heterogeneous datasets, collected from multi-modal sources, into an integrated dataset. This integrated dataset is supposed to be used for different types of medical analysis and unified decisions, using different machine learning approaches. -
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reynard
A novel universal genome assembly tool
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Online Signature Verification
Real time signature verification using MATLAB and C#
Online Signature Verification technology requires primarily a digitizing tablet and a special pen connected to the USB port of a computer. An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the... -
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CS Miner
A tool for Navigating in Chemical Space
CS-Miner stands for Chemical Space Miner and is a software tool for navigating in chemical space of compound databases. It helps for deriving appropriate classification models and performing virtual screening. Download it via: http://csminer.com/csm/?p=7 A quick tutorial is available through: http://csminer.com/csm/?p=8 -
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CUSHAW2: Parallel Gapped Read Alignment
One of the leading short-/long-read aligner to large genomes
CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. -
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FLASH
Merge mates from fragments that are shorter than twice the read length
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies. -
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FamSeq
Variant calling on the basis of pedigree information
It is still challenging to call rare variants. In family-based sequencing studies, information from all family members should be utilized to more accurately identify new germline mutations. FamSeq serves this purpose by providing the probability of an individual carrying a variant given his/her entire family’s raw measurements. FamSeq accommodates de novo mutations and can perform variant calling at chromosome X. To accommodate variations in data complexity, FamSeq consists of three... -
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PeptideManager_LRNO
Unique Peptide Sequence Finder (host background (xenografts) friendly)
PeptideManager is aimed to help the pre-selection of unique peptide sequences for the design of targeted proteomics approaches. Its main advantage is to allow the presence of a host/background proteome (e.g., xenograft samples) during this peptide sequences selection. PeptideManager can build peptide sequences databases from various public repository (SwissProt/Trembl/UniProt, RefSeq, IPI) and various proteases. For any use, please refer to the publication: doi:... -
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XNBC: neurobiology simulation tool
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site.