primedb is a project that attempt to generation prime numbers fast and saving them to a database(Mysql or else) for prime research: finding large number of prime,prime factorization,Goldbach's conjecture,twin prime conjecture...
An open-source quantum chemistry program package
PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models.
This program converts calculator-style ASCII math notation (the same that ASCIIMathML uses) to Spanish Braille mathematics notation (not Nemeth Code).
An RPN calculator for vectors of arbitrary dimension. Supports multiple undo/redo, programmable macros and variables. Saves/loads stack to/from disk. Lots of built-in scalar, vector, stack functionality.
PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".
Automated Sequence Annotation Pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible databases.
This is an extension to the standard 2D HF package (A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen and Dage Sundholm) that adds some extra functionality.
@Note2 is now available in www.anote-project.org @Note is a Biomedical Text Mining workbench that integrates current Biomedical Text Mining (BioTM) methods and provides biologists with intuitive tools capable of supporting their bibliographic searches and further literature curation.
ASSD is a simple biological sample database focused on the storage of proteomics data. It tracks every processing step incl. results throughout a sample's lifetime. Next to proteomics data it can also store other results like FACS or Western Blots.
AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
Algorithmic Based Automatic Contiguation of Shot-gun sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.
Convert a Garmin ADM database file to a GPX file
User data exported from later model Garmin GPSmap marine GPS sets consists of ADM files written to a VFAT-formatted SD card. This data includes user-generated waypoints and routes, and recorded GPS tracks. adm2gpx converts this data to industry-standard GPX records that may be imported into third-party mapping and GPS software.
A.I. security app. Development ceased.
APoDIx is a Portable Bio-Database Index system. It retrieves biological database information from the website of Oxford Journals, save them in a local position, and provides a viewer for display and search the information.
ASKGene (Automated Sequence Knowledge GENErator) - a customizeable integration platform for sequence-processing bioinformatics tools.
Assimilator is a molecular genetics tool to inform selection of associated genetic variants for functional studies
ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.
An AI irc bot that will interact with irc users.
Albion is a digital document archive presentation package. Features include a searchable database, an integrated spell checker, and automatic thumbnail generation. As native Perl as possible, the database/photos/search-function can be delivered on CD!
Symbolic Algebra using Perl
Algorithm::Evolutionary provides classes for performing simple evolutionary computation tasks, including definition of objects from XML and SOAP support. It should be interoperable with other EC libraries using SOAP.
Algorithm::MatchingModel is a perl library for running match simulations and statistics for two-sided matching problems. It includes classes for a preference factory, algorithm plug-ins, and gathering statistics between rounds.
A pipeline to define allele-specific genomic features
Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. Allelome.PRO offers increased sensitivity to analyse lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data.
A rule-based modelling framework for allosteric proteins and biochemical networks.
Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.