Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
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
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)
First automated tool for classification of transposable elements in eukaryotic organisms.
A program to identify Helitron given genomic sequences.
A fast efficient way of dealing with large amounts of Blast or Repeatmasker data.
A header file (cexcept.h) that provides Try/Throw/Catch macros similar to those available in C++ for error handling.
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.
PDFgetN is a program to process total scattering data obtained on neutron time-of-flight powder diffractometers and to obtain the atomic pair distribution function (PDF).
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph).
The OpenGEREA is a open enrichment analysis framework for gene expression regulation data analysis.
A.S.H. uses empirical correlations to generate scale-free network representations of protein relationships. These graphs are used to generated sub-networks and cliques which identify protein families and homologies.
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
Blast Explorer facilitates Blast results exploration
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?
Biological sequence analysis module used in generating CG clusters. Useful for basic sequence manipulations, regular expression based searches, and base compositional analysis.
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
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.
Bioinformatics software for analyzing the location of DNA motifs that induce self-catalytic depurination.
Continuation of the UCSB CS 290F class project.
FOCIS finds features for functional follow-up
FOCIS (Feature Overlapper for Chromosomal Interval Subsets) performs an interval-based screen of a database of genomic features – ChIP-seq peaks, motif matches, and others – for overlap enrichment at a specific subset of genomic regions relative to a dataset-matched background. It was recently used to discover a novel enhancer that mediates drug resistance in melanoma.
Scripts to implement Hierarchical Annotation-Dependent Alignment (HADA) protocol for sequence alignment, and related functions.
HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
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.