Search Results for "windows file manager"
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Showing 39 open source projects for "windows file manager"
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes... -
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure... -
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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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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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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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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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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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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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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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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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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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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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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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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 -
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CorNetMap
A tool for Gene Expression Correlation Network
Capabilities of CorNetMap: 1. Read data as tab-delimited text file. Can be used for analysis of any data set beyond gene expression. 2. Capable of both two-dimensional and multidimensional data analysis. 3. Calculate Pearson correlation and cross-correlation for analysis data with phase difference. 4. Generate correlation Heat-map and draws network map. 5. Save correlation data as text file. How to use and doccumentation:... -
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converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and...
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a... -
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caplib
Correct, translate and analyze combinatorial library sequencing data
Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file. -
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SpiKeDeteKt
An automatic spike detection program to be used with new KlustaKwik
This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs... -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An... -
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cancer_dynamics
Cancer Dynamics web
Website that shows the dynamics of a tumor by solving a system of ordinary differential equations. The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file.
