Search Results for "c-bus"
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21 programs for "c-bus" with 2 filters applied:
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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Updated 2022-06-11 added option to allow use of atoms other than C-alpha Updated 2021-11-29 to enable compilation on stricter compilers. Ab Initio protein structure prediction methods generate numerous structural candidates, which are referred to as decoys. Calibur is an efficient tool for finding the decoy with the most number of neighbors within a threshold distance. If you prefer to use GitHub, go to https://github.com/kalngyk/calibur
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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Patlac--Xml2cpp is a totally customizable code generator that generates classes (c++ for now) automatically from a xsd schema. Classes are described in google-ctemplate files and a xml options file allow precise definition of projects.
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by... -
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BayesAss
Bayesian Inference of Recent Migration Using Multilocus Genotypes
Inference of recent migration rates between populations using multi-locus marker genotype data. -
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Crux-Toolkit
Software toolkit for tandem mass spectrometry analysis
Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. If you use Crux in your research, please cite Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022--3027, 2008. -
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erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
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fast_count_multi
Extremely fast NGS read counter
... gtf_file bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x -
Secure remote access solution to your private network, in the cloud or on-prem.OpenVPN is here to bring simple, flexible, and cost-effective secure remote access to companies of all sizes, regardless of where their resources are located.
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ENLY
Bioinformatic tool to improve draft genome assemblies by closing gaps
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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. -
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Description: PseAAC-Builder is a cross-platform stand-alone program for generating protein pseudo-amino acid compositions. This is a bioinformatics program. It performs faster than the existing PseAAC server. Reference: [1] Pufeng Du, Shuwang Gu, Yasen Jiao. PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets. International Journal of Molecular Sciences 15 (2014) pp.3495-3506 [2] Pufeng Du, Xin Wang,...
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NHP-IMS
Non-Human Primate Information Management System
This project will enable a research lab using Non-Human Primates to control and track the Non-Human primates and the experiments associated with each. -
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BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.
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HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
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EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
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Bioinformatics software for analyzing the location of DNA motifs that induce self-catalytic depurination.
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Here is a repository of libraries automatically generated by Patlac::Xml2cpp software. All of these libraries are c++ translation of their respective xsd schema. They include classes with accessors, saxparser with iteration mode and xml serialization.
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Neurofitter is a parameter tuning package for electrophysiological neuron models. For more information please take a look at http://neurofitter.sourceforge.net
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SaskSAGE is package designed to exploit SAGE data. Csage is employed to identify and match SAGE tags in a biologically meaningful manner. Tags are analyzed for significance using a Chi squared test for independence between TAG and treatment.
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This is a collection of softwares that I have been using in my research on protein interaction network. By release them under the GPL 2.0 lience, I hope that they can be useful to others, as well.
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