Search Results for "tree file" - Page 2
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Showing 62 open source projects for "tree file"
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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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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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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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TCellXTalk
TCellXTalk Web-App from LP CSIC/UAB
TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and... -
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Nelder Plot Designer
A Computer-aided Tool for Nelder Plot Design
Nelder plot (Nelder 1962) is an experimental design for testing a multiple tree spacings in a single plot. The shape of plot is circular with some number of concentric wheels or arcs radiating outward and the spokes connecting the center. The intersections of spokes and arcs are the tree positions. The tree position on different wheels represent a different the tree spacing distance or tree density. This design eliminates the need for separate experimental plots for each tree density. The... -
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EfiPy
Python Library for accessing UEFI BIOS internal function by protocol
EfiPy is a Python Module on UEFI shell which can access UEFI BIOS kernel interface - System Table - Runtime Services - Boot Services pAnalyzer package - Tracing UEFI protocol calling flow Output protocol flow to screen or file with XML format CorePy (assembly package) - Simple Assembly code in Python environment. EfiPy Shell package- Simple uefi shell program coded with EfiPy library to prove EfiPy workable EfiPy leverage these open source packages - ctypes, CorePy. Samples https://sourceforge.net/u/efipy/svn/HEAD/tree/Trunk/ EfiPy Author: https://www.linkedin.com/in/max-wu-a9068b90/ -
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PdfCMYKerLite
PdfCMYKerLite - inspect and remix CMYK separations of PDF file
PdfCMYKerLite is a wxPython GUI front-end for Ghostscript `gs` and ImageMagick `convert`, which uses the Ghostscript tiffsep device to obtain CMYK separations of a PDF document. For full description, see README.md in the code browser at https://sourceforge.net/p/pdfcmykerlite/code/ci/master/tree/ -
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting... -
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Analyzer for Files
A tool to look into file contents
Analyzer for Files (AoF) is a tool to look into file contents, analyze the structure with installed plug-ins, and show the results with several split windows including converted data and a tree if successful. It was designed as a workbench with a core and plug-in extensions. It can handle the normal plain-text file and data, complex binaries supported with the corresponding plug-ins. -
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IncludeGraph
Determine which files get included in source files.
IncludeGraph is a tool written in Python that performs code analysis on a C and C++ source tree. It can determine the inclusion path for a header file as well as provide charts about which headers are the most included ones or which files include the most headers. It also has a limited knowledge of conditional preprocessor constructs by implementing a subset of the functionality of the C preprocessor. -
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Music Merge Manager
Identify duplicate songs based on track metadata (ID3, etc)
Given two trees of audio files, examine the metadata for each file to try and determine the differences in the content of the trees. This helps find duplicate songs (or non-duplicated songs) even if the music is stored in different formats. Toggles let you determine how specific the matching criteria must be: Track number and song name? Artist, album, and track length? All of the above? Ultimately this program will let you delete duplicates from either the left or right trees, or copy non-duplicated files from one tree to the other. ... -
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simplex with branch and bound
A tool for teaching simplex and branch & bound methods
This is a tool for teaching simplex and branch & bound methods. For simplex method, it comes with several examples including degeneracy and cycling, and allow the user to dictate how to pivot. For branch and bound method, it is desinged to interact with the user to explore all possible branch and bound trees. The user can also load a problem from a text file or simply type in a model directly. The format is very simple and very similar to the LP format, see the packed-in examples. -
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pyMantis is a data-management system for (systems) biology build on the web2py framework. It features: tree based file explorer, relational db table wizzard with automated creation of user interfaces, internal and external access management, wiki, ..
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Patchamama is a binary patch maker/applier that works on directory tree. It can be used in application deployment, large scale project patching (including source and binary data). It use bsdiff for the binary diff job and 7zip for compression.
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t2t-pipe
automatic alignment pipeline for parallel treebanks
The *Tree-to-Tree (t2t) Alignment Pipe* is a collection of python scripts, co-ordinating the process of automatic alignment of parallel treebanks from plain text files with a single call from a unix command line. Supported Languages: DE, FR, EN -
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gEcrit is a Python orientated source code editor. It tries to keep the interface as clean as possible and keep the menus simple. It features all the common features a Python programmer might need, including an interactive Python shell.
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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 unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. ... -
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HTML DOM Parser
HTML parser which can be used for screen-scraping applications
htmldom parses the HTML file and provides methods for iterating and searching the parse tree in a similar way as Jquery. To report bugs please mail me at bhimsen.pes@gmail.com -
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Create Launcher
Creates a .desktop launcher for the Linux menu system
This project is to develop a GUI/graphical way to create a .desktop file. Whereas alacarte can be used to do this, alacarte requires multiple creation of several launchers if one wants them in several menu areas. The menu specification allows one .desktop file to lists more than one menu location. This project doesn't support all possible .desktop formating choices, but allows the basics for someone who has a wine file, or some other program they would like to launch graphically to easily... -
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Naufrago! is a simple offline RSS reader (including images) written in Python.
