Search Results for "base-files" - Page 9

A perl script that converts Illumina qseq files into Phred fastq files for use in Maq. Originally written by Tyler Bachman from UC Riverside, adapted by Eugene Goltsman. Freely available under the terms of GNU GPLv3.

mzSquash is a compression tool for mzML files, an XML-based standard developed by HUPO PSI (http://www.psidev.info) for spectrometer output. All development has ceased. The tool may be useful educationally, but is not a recommended utility.

PeptideProphet and ProteinProphet CGI program source files modified to make interoperable with Rosetta Biosoftware's Elucidator(R) System. All files are published and distributed under the LGPL license, v2.1.

The Shrimp suite provides interactive visualizations of graph-based data. Creole (Eclipse plug-in) visualizes Java source code. Jambalaya (Protege plug-in) visualizes ontologies (including OWL), & Stand-Alone Shrimp visualizes RSF/GXL/PRJ/PPRJ files.

User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files

EXPR is a software package for the recording and analysis of animal behaviour. Recording is done by pressing particular keyboard keys on the computer. The software then saves the sequence and timing of behaviours. Note that the DOS (1995: https://sourceforge.net/projects/expr/files/expr/fb-port-expr-00-1995/EXPR-binary-DOS-0.0.1995.tar.gz/download) version is currently the only fully functional and is recommended for use. On modern computers, DOS software can run in DOSBOX (https...

splitsmb is a standalone application for calculating topological convergence diagnostics on MrBayes tree-output files (unrooted only at this point). It calculates the average- and maximum standard deviations of partition frequencies between runs.

sbmlop is a command-line utility to create, view and manipulate SBML (the Systems Biology Markup Language). It is ideally suited for operating on large batches of SBML files, and can extract and modify information using regular expressions.

Design tool for multiplex Polymerase Chain Reaction (PCR) Single Base Extension (SBE) genotyping assays.

A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.

The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.

BioStream enables bioinformatics researchers to create, query and apply tools to their own databases. It supports sequence files and other data types by allowing the creation of metadata definition files.

Adamant is a java application for annotation of microarray array designs. The software enables MIAME-compliant annotation of sequences spotted onto arrays and can produce output files in MAGE-ML and other data formats used by public microarray data repos

TrypC was developed for digesting protein sequences into peptides using fully, semi, and nontryptic cleavage conditions. Associated libraries allow direct loading of data from FASTA files.

Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

aln2dist is a standalone program that uses a multiple sequence alignment to calculate a set of distance matrices and a set of distance restraints (lower and upper bounds). Also require the pdb structure files of homologous proteins to be used as models.

The field representation projectis based on the Field Representation Language (FRL) and associated tools. Primarily this means the Abstract Field Layer (AFL) - a C++ API for reading, manipulating and writing FRL files.

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.

Genetic programming environment to inference context free grammars base on positive and negative examples of language.

Perl module for reading/writing QuickBooks IIF files.

NEV2lkit is a tool for handling neuronal event files.

SeqTRACS is a Laboratory Information Management System for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. Trace files are tracked in a database and can be retrieved by users

Io (ISREC ontologizer) is a program to classify high-throughput genomics data (e.g. microarray results) in the Gene Ontology. Io includes a statistical estimation of the significance of data in the GO nodes and reannotation files for Affymetrix chips.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

BioNote is a knowledge base that combines unstructured wiki technology with structured annotation to form a collaborative environment. BioNote adds the concepts of page types and semi-structured annotation to extend the unstructured nature of wiki pages