Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
This project will hope to provide an application (using the Java coding language) that will manage facts and citations used in writing research reports. The application will have the ability to manage facts and create citations in accepted formats.
The OpenGEREA is a open enrichment analysis framework for gene expression regulation data analysis.
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time.
Biological sequence analysis module used in generating CG clusters. Useful for basic sequence manipulations, regular expression based searches, and base compositional analysis.
The HyperGlossary Project enables real-time annotations of web sites for the purpose of explaining jargon-heavy pages with pop-up definitions and other resources, such as powerpoints and videos.
Blast Explorer facilitates Blast results exploration
SimBac is a software package for simulating bacterial genome evolution. It outputs samples of DNA sequences at each generation & allows testing of major evolutionary mechanisms, including mutation, recombination, genetic drift, and natural selection.
The ideal Operation System, BioInfoServOS, which is a specially customised system for scientists handling and analysing biological data, but also for easy use of daily official business handing, has been distributed. Offcial Website: [http://edu.bioinfoserv.org] (edu.bioinfoserv.org)
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).
A virtual software pipeline that contains several PERL modules for processing next generation sequencing data
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.
RIPCAL is a bioinformatics tool for the analysis of repeat-induced point mutation (RIP) of fungi. If you publish work using RIPCAL please cite: Hane & Oliver, BMC Bioinformatics 2008, 9:478
Linux utility scripts
A handy set of Linux utility scripts. Mount a remote Windows share, display the processes associated with a pty, distribute .rc files or ssh public key to clients, tunnel RDC or VNC through remote gateway via ssh, easy command-line access to system config tools, and more.
uDOS is a free operating system built on the FreeDOS kernel with DJGPP. uDOS provides an integrated suite of features inluding Perl, Python, etc., as well as a Watt-32 based networking environment and ELF library support. Can be run live from CD image.
iCamp is a research and development project funded by the European Commission. The project aims at creating an infrastructure for collaboration and networking in Higher Education across systems.
The idea of this project is to create a php user friendly interface for traffic shaping. It lets the network administrator manage internet traffic, network services, internet protocols...The object of this project is to ensure the QOS of the network.
Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. Suitable for mammalian repertoire sequences obtained either by Sanger or 454 sequencing. Methods published in Glanville, Zhai, Berka et al, PNAS 2009.
Selects SNPs and samples with known genotypes for microarray design
Program apply linear programming to minimize the number of microarrays and hybridization experiments that need to be undertaken in order to cover most of the predicted expressed SNPs.Dependencies:. 1) mampl.exe must be in system PATH 2) CPLEX 12.2 must be installed. cplexamp.exe must be in system PATH mampl.exe can be obtained from any program containing AMPL. I obtained AMPL from trial version of MOSEK at http://www.mosek.com/. CPLEX 12.0 can be obtained from http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/. A free acadamic license can be obtained by filling out IBM academic initiative application.
D.U.C.K (Determine segmentation of Unknown words by using Context Knowledge)is an NLP tool, which aims to find the correct segmentation for unknown words in written Hebrew. Statistics from different scopes will be used to determine the segmentation.
CNV-WebStore is an integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Contact system admin at http://cnv-webstore.uantwerpen.be for installation scripts
ChIPOTle is a peak-finding algorithm used to analyze ChIP-chip microarray data
This software is a Perl Catalyst based electronic lab notebook (ELN) aiming for small biologic laboratories, that have no funding to invest into a closed source ELN.
BLibrestez Robotics Software Library Project
http://sourceforge.net/feeds/p/PROJECT-BLIBRESTEZ55ROBOTICS/issueupdates/basic BLIBRESTEZ55ROBOTICSPROJECT/downloads/basic http://sourceforge.net/feeds/p/PROJECT Copyright©2011-2020 BLibrestez55Ro
I often encountered an inability among users to think beyond SAP and MS. Goal of the project is to create a web based application management platform, which enables organisations to easily manage applications within the system.