Search Results for "ghost 4 linux"
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Showing 42 open source projects for "ghost 4 linux"
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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JRC QSAR Model Database
(Q)SAR Model Reporting Format Inventory
In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf... -
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TVscript
Exploration of the removal of count variable transcripts.
> See TVscript wiki: https://sourceforge.net/p/tvscript/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: (See wiki) 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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PPIXpress
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal... -
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MELTING is a software to compute, for a nucleic acid duplex, the enthalpy and the entropy of the helix coil transition and then the melting temperature. Four types of hybridization are possible : DNA/DNA, RNA/RNA, RNA/DNA and mRNA/RNA.
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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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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do... -
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The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.
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This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.
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ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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ToxOtis is a Java interface to the predictive toxicology services of OpenTox. ToxOtis is being developed to help both those who need a painless way to consume OpenTox web services and for ambitious service providers...
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gfit creates an interface between computational models and experimental data and provides tools for their analysis
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primeHandle is a set of data management tools in support of the PrIMe Initiative (http://primekinetics.org). primeHandle includes graphical user interfaces for searching through data collections, editing and submitting data to the PrIMe Data Depository.
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ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.
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DEPRECATED PROJECT! SolexaTools is becoming the SeqWare project (http://seqware.sourceforge.net) to better reflect its expanded sequencer support. Please go to this project page for code and documentation.
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A sorting tool for Bioinformatics, Biochemistry and/or Molecular biology. This sorts nucleotide sequences aligned using "ClustalW". There may be a way to do this w/ original app, but someone I know couldn't figure out how - thus this project was born
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A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.
