Search Results for "simple files"
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Showing 27 open source projects for "simple files"
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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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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other... -
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Wordom is a (simple) command line utility conceived to spare the user some time in manipulating, converting and analyzing molecular structure and molecular simulations files. Due to its simplicity, it is easy to add your own analysis module.
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab-delimited text, Percolator pin, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net -
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Quadric
Application for simple base-2 binary to base-4 DNA-code conversion
Quadric is an opensource file converter created by the Jomcraft Network development team. In it's core functionality this small utility can transform base-2 binary files into base-4 DNA-coded human-legible ASCII-files. -
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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DicomReader is a simple Java Dicom files decipher. It handles headers and images within as well; data (headers and pixel-value images) will be saved into ascii clear text files. A pgm version of the image files is also provided.
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mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
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The Wily DNA Editor
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section. -
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BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. ... -
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bsclient
An interactive FTP-like command-line BaseSpace download client
bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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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 clade-defining polymorphism. This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID -
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Snp Viewer
A program for visualising Affymetrix SNP array data
A program for visualising Affymetrix SNP array data for identification regions of homozygosity. Written to aid autozygosity mapping and aid the discovery of potential disease loci. -
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noise-free-cnv
program for analyzing and manipulating DNA microarray data
...Direct inspection of the microarray data with the noise-free-cnv software helps to appreciate the quality of the data and to identify artificial calls. With noise-free-cnv it is possible to visualize individual datasets, to compare different datasets and to perform simple transformations. The visualization and the suppression of genomic waves, the comparison of two datasets by subtraction and the simultaneous inspection of LRR and BAF values are amongst the most frequent applications of this software. This program is able to read and write files suitable for PennCNV or raw files containing measured values of any kind. -
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...Note that the 2.0-1 version is delivered as a source (*.tar.gz for Linux and Mac users) and as a binary file (*.zip, for Windows users). The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy from https://sourceforge.net/projects/rawgeno/files/rawgeno/RawGeno%202.0-1/ Make also sure to have a look at https://sourceforge.net/projects/rawgeno/files/ where you can find a detailed manual, demo datasets and many demo scripts.
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samscope
A lightweight OpenGL SAM/BAM viewer
A lightweight OpenGL based interactive SAM/BAM viewer. Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. -
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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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A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.
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Adjusting PKL-Files derived from MS-experiments. The development of the project has been MOVED TO https://github.com/binfalse/adjustpkl
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These scripts written in Python allow you to convert fasta files into multifasta file and vice versa.
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BioDOM is a JAVA library for easy creation of XML files according to simple XML schemas for describing biological data. It can also be used to convert other commonly used biological (possibly non-)XML data into these new formats.
