Search Results for "code source ping" - Page 2
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Showing 99 open source projects for "code source ping"
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
...To build a source package of MANTIS, use the script buildPackage.R To install MANTIS use 'install.packages(file.tar.gz,type="src",repo=NULL)' To test use test_V3.3_code.R Contact the main author of the publication above for further details. Have fun! -
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CSBB-v2.1 [CSBB-v3.0 is now available]
Computational Suite For Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and... -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,... -
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This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
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CNVMM
CNVMM performs copy number variations detection
CNVMM specializes in identifying copy number variations (CNVs) when there are repeated sequences in the reference genome. The input file is a single short read mapping result from any short read aligners. However, NNmapper or Bowtie2, which detect all mapping results for multi-reads, are recommended. To use the code, MATLAB installation is required. Mac or Linus system is required. -
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EFO
The Experimental Factor Ontology describing experimental variables
*** Please note this repository is now deprecated as of January 2018. All EFO development and source code has been moved to https://github.com/EBISPOT/efo *** The Experimental Factor Ontology (EFO) available from http://www.ebi.ac.uk/efo is an application focused ontology modeling the experimental factors in ArrayExpress and constructing mappings to multiple existing domain specific ontologies. To submit new terms, features or report bugs please submit a ticket at the following: http://www.ebi.ac.uk/panda/jira/secure/CreateIssue!... -
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CSBB-v2.0
Computational Suite for Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and... -
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WrapImaJ
Multi-platform API for Image Processing systems in Life Sciences
...The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. In it's current form, it only wraps basic functionalities of ImageJ. The developers of WrapImaJ intend the library to support compatibilty with the main imaging systems available in the Java language and broadly used in the field of life sciences. -
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PBSuite
Software for Long-Read Sequencing Data from PacBio
This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to... -
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INTEGRATE: Calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. To download source code, reference manual and test case, please go to 'Files'. Also refer to 'Wiki' for details.
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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GNomEx
A Genomic LIMS and Data Repository
Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. -
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....: "HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. HeatmapGenerator is released under the GNU GPL.
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PromKappa 2.0 (DNA patterns in Java)
PromKappa 2.0 (Java source code and bin)
A Java adaptation of DNA patterns based on the article "Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters". by Ilie Guta (Java source code for DNA patterns) -
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Moose
Multiscale Neuroscience and Systems Biology Simulator
Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes. We have moved Github.com. This should be your source for the latest version of the code. -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic,... -
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...In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format. The software source code is freely available under the license of GPL2.
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Madeline 2.0 Pedigree Drawing Engine
Madeline 2.0 Pedigree Drawing Engine (PDE)
The Madeline 2.0 Pedigree Drawing Engine is a pedigree drawing program designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. PLEASE NOTE THAT as of 2015.09.30, the most current Madeline source code tree is now maintained on GITHUB at https://github.com/piratical/Madeline_2.0_PDE . -
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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
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DEAPathways
Differential Expression Analysis for Pathways
This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967 -
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Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
Ours organization website GCModeller.org is coming online soon! Shoal Shell is the sub project for the "genome-in-code"(http://code.google.com/p/genome-in-code/) virtual cell modelling project of the bacteria Xcc 8004. Shoal Shell aim at provide the modelling tool and the debugging tool for the GCModeller virtual cell modelling, And from the extendible library package, shoal shell can manage to accomplish the entire modelling job for any other bacteria species. Shoal Shell Project... -
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
...Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." *Please cite this paper if you use this code for your research -
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The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
