Search Results for "python windows" - Page 2
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Showing 304 open source projects for "python windows"
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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics... -
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SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.
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SASA Tool
SWATH-Auto System Analyzer Tool, SASA Tool
SWATH-Auto System Analyzer Tool, SASA Tool, is a novel SWATH platform for non-targeted metabolomics data analysis with an accurate mass spectral library for metabolite identification using SWATH acquisition mode. -
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SBW (Systems Biology Workbench)
Framework for Systems Biology
The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as... -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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ECOLOG
A database management system for ecological field surveys
ECOLOG is a specimen-based, cross-platform relational database management system, aimed at the storage, retrieval and preliminary analysis of data on sites, species, and specimens gathered in ecological field surveys and biodiversity inventories. The main goal of ECOLOG is to make the data gathered in ecological field surveys readily accessible, providing lists of species collected in the study area and informations on habitat preferences, abundance or rarity of a given species, biometrics,... -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
MAGeCK2 is here: https://github.com/davidliwei/mageck2 Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at... -
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Xmaldi
Viewing collections of MALDI spectra and perform PCA and DFA analyses
Xmaldi is an application for viewing collections of MALDI spectra and perform PCA and DFA analyses on them (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/xmaldi3/code/ci/default/tree/README.md -
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JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
Visor for mass spectrometry JSON files generated by the Integrator program (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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LaiaMotifs
Search for MHC-like motifs in peptide collections
Search for MHC-like motifs in peptide collections (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/laiamotifs3/code/ci/default/tree/README.md -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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geostd is an open-source set of restraints for molecules involved in macromolecular structure refinement. The restraints reduce the number of variables making the solution of protein structures a more tractable process.
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Peptide Vaccine Analysis Tool (PVAT) is an optimization software that predicts the best possible peptide stretches in a given protein sequence based on two factors: 1. the surface exposure of the peptide stretches, and 2. their susceptibility to mutation.
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome... -
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bioweb
polyglot language framework to analyze genetic data
polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences -
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parent-map
Analyze parental contributions to evolved or engineered protein or DNA
Documentation: https://parent-map.readthedocs.io/ -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this... -
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CBMPy
PySCeS Constraint Based Modelling
PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently... -
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MGFVisor
Visor for mass spectrometry MGF files
Visor for mass spectrometry MGF files (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/mgfvisor3/code/ci/default/tree/README.md -
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Python4Proteomics Course
Python course for Proteomics analysis
Python course (in Spanish) for Proteomics analysis using basically Jupyter NoteBooks. For more information, you can have a look at the readme.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/p4p/code/ci/default/tree/readme.md -
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EasierMGF
Converts RAW Thermo Files into MGF files
Converts RAW Thermo Files into MGF files (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/easiermgf3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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TagCalc
Calculates groups of aminoacids that adjust to a mass difference
Calculates groups of amino-acids that adjust to a mass difference (Python 3 version). -
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KimPeptid
Analyzes Peptides Properties (Python 3 version)
Analyzes Peptides Properties (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimpeptid3/code/ci/default/tree/README.md
