ProPHAnE: Proteomics result Pruning and Homology group Annotation Engine A perl script based workflow for annotation of protein data coming from the 'Mascot' (Matrix Science) and 'Scaffold' (Proteome Software) pipeline. Coming soon: Prophane 2, "a much improved and extended version of Prophane based on HTML5, PHP and MySQL. Most importantly, the pipeline includes now functional predictions on profile Hidden Markov models (HMMs), is fully-automated, and can be controlled via a highly intuitive and user-friendly interface." (Stephan Fuchs)
Bioinformatics tools and scripts to help analyze protein and nucleotide data through the use of Hidden Markov Models (HMMs). These will involve scripts, conversion programs and data to support the upcoming book, 'Hidden Markov Models for Bioinformatics'.
A HMM-based algorithm for defining enriched regions from ChIP-seq data
HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles note: 1. Default species is HUMAN. Also supports MOUSE. Can add any other genome if in need. 2. Default format is BED. Also support ELAND. Will add SAM and BAM. 3. –r specifies read length (this is import through my experience). 4. –pe indicates pair-ended data. 5. If data is pair-ended, -isize refers to insert size (total length of a pair).
Typical Web Firewalls use a mechanism to classify anomaly traffics. This tool submits an old-school malicious (not dangerous) request, and tells you the type of firewall a particular web site use (if any). Mainly useful for blackbox security assessment
DNAtools is a perl CGI based software wich analyzes DNA sequences in order to find out the maximum of information for further bio analysis. It is intended to help people to gain time.
Written in perl, mWayToGo, converts palm database files (.pdb) created by the Magellan Nav Companion GPS software to comma delimited lists of waypoints. The lists include date of creation/editing, name/desc, lat, long, and height.
Wordgen is a perl script for automaticaly generating a random character sequence based on a rule set. The rule set is specified in a flexible description language. Its main purpouse is automatic word generation for conlanging but may have other uses.
A customisable web form to deposit metadata about research datasets into a Fedora repository. Based on open source VALET software, this tool was developed at UNSW Library. This project is supported by the Australian National Data Service (ANDS).
Italian language pack for Bugzilla
Get specific sequences from a multi-FASTA file.
A command-line utility to manipulate biological sequences from a multi-FASTA file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only.
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)
mpiGraph is designed to inspect the health and scalability of a high-performance interconnect while under heavy load. This is useful to detect hardware and software problems in a system, such as slow nodes, links, switches, or routing contention.
Encode Arabic provides tools for encoding and decoding Arabic in Haskell, Python, Perl, or LaTeX. Interprets the ArabTeX notation to generate original orthography or phonetic transcription. Supports Buckwalter and other romanizations. Converts legacy byte encodings into Unicode. http://github.com/otakar-smrz/encode-arabic
Functional Arabic Morphology
ElixirFM is a high-level implementation of Functional Arabic Morphology. The core of ElixirFM is written in Haskell, while interfaces in Python and Perl support lexicon editing and other interactions. http://github.com/otakar-smrz/elixir-fm
NIUS allows reservation of nodes under it's control for exclusive interactive use by a group of users. This system is in use by National Center for Data Mining at University of Illinois in Chicago to reserve workstations for researchers.
A hidden Markov model to predict clustered RNA motif sites
Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large number of in vivo RBP binding sites obtained from high throughput sequencing of RNAs isolated by cross-linking and immunoprecipitation (HITS-CLIP). We applied this algorithm to study two representative RBPs, Nova and Mbnl. Despite the very low information content in individual motif elements, our algorithm made very specific predictions for successful experimental validation.
bib2html convert BibTeX descriptions of publications into a set of html pages with several different index pages types. Formatting is controllable through XSL.
ArielCLUSTER is a very tiny implementation of PVM architecture, written in perl.
Simple Logging InfiniBand Infrastructure
The Glasgow Symmetry Reduction tools are a suite of software tools providing symmetry reduction for the SPIN and PRISM model checkers. The main tools are TopSPIN and GRIP. The suite also includes Etch, and enhanced type checker for Promela.
trolL - the traffic alLocator for end-to-end model reservation for semi permanent connection
A suite of BioPerl wrappers for manipulating DNA and protein sequences
DNATweezer is a suite of Perl scripts for manipulating DNA and proteins sequences. These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences.
LatexInWord provides macros for Microsoft Word that allow the use of LaTeX input to create equations images in both inline and display modes. Similar macros for other word processors will hopefully be added in the future. We are currently in the process of migrating this project to GitHub: Client: https://github.com/EngineeroLabs/latex_in_word Server: https://github.com/EngineeroLabs/Process_LaTeX
Ensembl Easy Sequence Retriever
Maldonado E, Khan I, Philip S, Vasconcelos V, Antunes A (2013) EASER: Ensembl Easy Sequence Retriever. Evolutionary Bioinformatics, 9:487-490. doi: 10.4137/EBO.S11335.