A collection of Perl modules for handling fasta/q sequences and files.
WARNING: BioUtils has been migrated to Github (Nov 2017). For the most up-to-date versions and info please visit: https://github.com/islandhopper81/BioUtils BioUtils are a collection of Perl modules for DNA sequence analysis in bioinformatics. BioUtils is a significantly faster and more memory efficient alternative to BioPerl. However, it's functionality is currently limited to the features listed below.
Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.
Simple small tools for bioinformatics written in bash perl and python
This is a small project providing simple yet useful scripts for miscellaneous bioinformatics tasks. Powered by the BioInfX team of the Department of Genetics and Molecular Biology of the Center for Research and Advanced Studies of the National Polytechnic Institute of Mexico.
An Ajax based Functional Genomics Application Server to aid in functional analysis of entire genome in-silico.
Biolet is project aimed to analyze genomic DNA sequences using wavelets. Of additional interest may be a batch processing tool for doing round-robin scheduling of jobs on a beowulf cluster. For that checkout the project robin from the CVS.
A collection of corpus and access routines for developing biological literature analysis systems.
This is a collection of softwares that I have been using in my research on protein interaction network. By release them under the GPL 2.0 lience, I hope that they can be useful to others, as well.
The Biomolecule Naming Service (BNS) is loosely inspired by DNS servers used to resolve host names and IP addresses. BNS uses the Lightweight Directory Access Protocol (LDAP) to resolve gene/protein names and identifiers.
Biosysplus is a software which use to generate ordinary differential equations for large scale molecular network. User just only need to provide some key reaction step and rate constant.
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj
Blast Explorer facilitates Blast results exploration
Boardstatus is a Web-CGI/Postgresql database to manage electronic prototypes, including butch lists, notes, and and parameters. Support for users with different authorizations is included.
Bobware tool suite is a set of small EDA tools which are useful in the design of integrated circuits. The suite contains a perl/tk script for region planning large ASICs (application specific integrated circuits.)
BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
Simulate the structural and copy number consequences of BFB
BFBsimulator simulates the structural and copy number consequences of breakage fusion bridge (BFB) cycles in silico. Hundreds of aCGH profiles of many different tumour types are now freely available and many of these newly surveyed genomes contain amplified oncogenes. The most commonly cited explanation for the processes underlying gene amplification is the the repeated fusion and breakage of chromosomes following the loss of a telomere. However, this proposition has never been fully investigated. Using BFBsimulator, we can ask: i) Can the complex patterns of amplification within cancer genomes really be generated by BFB cycles? ii) What visible effect might BFB cycles have on tumour copy number profiles? iii) Is there a specific copy number ‘signature’ of evolution though breakage fusion bridge cycles? iv) What is the prevalence of BFB cycling across different cancers?
A national virtual bridge engineering contest for kids of all ages.
A national virtual bridge engineering contest with prizes for middle and high school kids, grades 6 to 12, but anyone can enter for fun. Based on the award-wining Bridge Designer client software, now open source through this project. Web site infrastructure supports worldwide participation in qualifying and semifinal rounds with a tiny administrative staff. The new Rails back end is a RubyMine project. Thanks to JetBrains for this awesome development environment!
A national virtual bridge engineering contest for kids of all ages.
**Unfortunately, the Bridge Contest is no longer operational. We hope the code base will be of use to others with similar projects in mind.** A national virtual bridge engineering contest with prizes for middle and high school kids, grades 6 to 12, but anyone can enter for fun. Based on the award-wining Bridge Designer client software, now open source through this project. Web site infrastructure supports worldwide participation in qualifying and semifinal rounds with a tiny administrative staff. The new Rails back end is a RubyMine project. Thanks to JetBrains for this mega development environment!
OpenBRR is an initiative to create an open and standard framework for software assessment process. We strive to provide the industry standard framework in the open source world, and also the trusted data source to aid software assessment process.
Scripts for parsing and general use in Computer Forensics - Octane Lab
O projeto Byte Investigator do Octane Labs nasceu com a finalidade de se ter um kit de ferramentas (scripts perl) de parsing de varias estruturas do ambiente Windows (arquivos e estruturas dos file systems). Estas ferramentas poderão ser utilizadas no cotidiano dos profissionais e pesquisadores de segurança nas tratativas de resposta a incidentes de Segurança de Informação e Computação Forense. A técnica de parser ou parsing consiste em usar um programa que detalhe as informações contidas em uma estrutura, seja ela de um arquivo do sistema operacional (por ex, um .lnk), de um arquivo de um aplicativo (por ex, um .ppt) ou mesmo de uma estrutura do próprio sistema (por ex, o $I30). Byte Investigator The Byte Investigator project from Octane Labs was born in order to be a parsing toolkit for several Windows structures (files and file system structures). These Perl script tools are useful tools for Computer Forensics professionals and Information Security researchers.
C-squares is an easily implemented method for storage, querying and display of spatial data locations, based on a hierarchical, grid-based representation of the Earth' surface. Source code for encoding, decoding, mapping, etc. is provided via this site.
Classification Algorithm Based on a Bayesian method for Genomics
CAPE stands for Clips And Perl with Extensions. As its name suggests, CAPE is a combined programming environment which allows programs to be written in Clips, a forward-chaining rule-based system which was originally developed by NASA, and Perl.
Classification based Analysis of Paired Expression data of RNA
CAPE RNA is package of command-line tools for integrated analysis of miRNA-mRNA expression data. miRNA-mRNA interaction states are assigned for each sample independent of a priori known experimental groups. Using these interaction classifications Jaccard-indexes are calculated to evaluate the quality of a predicted interaction based on the distribution of assigned interaction states compared to experimental groups. In addition, negative correlation between miRNA and mRNA expression can be analyzed.
Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab