Search Results for "shell script library"

DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom...

PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create).

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format

LBXR - LOAD BLAST XML RESULTS O sistema permite que sejam importados resultados obtidos por meio de pesquisas de similaridade a partir do BLAST, com resultados gerado no formato XML para o banco de dados relacional MariaDB ou MySQL.

ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD...

Here we present an image-based Multi Channel Classification and Clustering System (MCCCS). It is an generalized, script-based classification system for processing various kinds of image data. Due to the modular design, individual processing-components can be easily adapted, extended or exchanged by own extensions. See project website for installation instructions.

...Shoal Shell Project needs grownup I'm just a student in the university, and the shoal shell just in its begining, if you have any idea about shoal, please contact me from xie.guigang@gmail.com. The Shoal shell needs your professional advice. Try get some help (if you want build the shoal library by yourself): https://sourceforge.net/p/shoal/wiki/Shoal%20Developer%20Guide/

Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.

OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method. It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs...

parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A...

If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge

cifget is a DDLm dictionary import expansion utility, which generates expanded dictionaries that could be used when reading, writing, or validating CIF files

BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.

(OBSOLETE) trace_utils is a program for processing sequencing trace data. The main goal of this program is to provide a completely free software in detecting SNPs like what polyphred has done, but with even higher accuracy and more flexibility.

'torungmx' is a script to help you running Gromacs