Planfix: Manage Projects, Team's Tasks and Business Processes
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The program consgen takes multiple protein structures in PDB format and aligns them using a modified Procrustes method that aims to maximize residue similarity. The principal result is a consensus structure showing residue conservation.
Xipe-Totec is a companion program to the paper
"An application of statistics to comparative metagenomics"
by Beltran Rodriguez-Brito, Forest Rohwer and Robert Edwards
BMC Bioinformatics 2006, 7:162
doi:10.1186/1471-2105-7-162
Cleaver is a program for comparing restriction endonuclease digests of orthologous DNA sequences from different taxa. It performs virtual restriction digests and searches for endonucleases that cleave DNA fragments from given taxa but not others.
Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program.
It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user
written MAEPlugins, documentation, tutorials, demo data.
With ThinkAutomation, you get an open-ended studio to build any and every automated workflow you could ever need.
When a message is received ThinkAutomation automatically executes one or more Automations. Automations are created using an easy to use drag-and-drop interface to run simple or complex tasks. Automations can perform many business process Actions, including: updating company databases, CRM systems and cloud services, sending outgoing emails, Teams & SMS messages, document processing, custom scripting, integration and much more. Over 100 built-in actions are included, plus ThinkAutomation is extensible with Custom Actions.
ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.
SIP (Sample Inventory Program) is a web application for managing mass quantities of lab samples. It is the first out-of-the-box Zope 3 app, and is field-proven.
SIP may be used as-is, or as inspiration for other Zope 3 apps. (e.g. O/R RDBMS storage)
ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)).
The modern employee engagement platform for the modern workforce
Create a positive and energetic workplace environment with Motivosity, an innovative employee recognition and engagement platform. With Motivosity, employees can give each other small monetary bonuses for doing great things, promoting trust, collaboration, and appreciation in the workplace. The software solution comes with features such as an open-currency open-reward system, insights and analytics, dynamic organization chart, award programs, milestones, and more.
SpOK - The Spectrum Organisation Kit, a program for the organisation and visualisation of spectral data written in Java. Sorry - this project is not being continued. All functionality was integrated into the Bioclipse project...
Io (ISREC ontologizer) is a program to classify high-throughput genomics data (e.g. microarray results) in the Gene Ontology. Io includes a statistical estimation of the significance of data in the GO nodes and reannotation files for Affymetrix chips.
MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
The phase machine program allows supervised classification of DNA sequence data from different populations using haplotype sequences generated by the PHASE program.
A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc
ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.
Phight - a phylogeny tree building program
Currently, it supports Likelihood method and distance method. This program will includes diagnostic function as a special feature.
The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
(OBSOLETE) trace_utils is a program for processing sequencing trace data. The main goal of this program is to provide a completely free software in detecting SNPs like what polyphred has done, but with even higher accuracy and more flexibility.
ReadSeq is a program and library for conversion of biosequence data from one format to another, useful in various bioinformatics programs and services. It is written in Java, though an earlier version in C remains available.
Bio::Prospect:: is a Perl API to the
PROSPECT threading application. The modules provide for program
execution, results parsing, multiple sequence alignments inferred from
pairwise sequence-structure alignments, and rudimentary homology models.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
GenomePixelizer is a program for comparative genomics, detection of duplication events in genomes, tracking the "footprints" of evolution. It may be considered as a drawing tool that generates custom images of genomes out of the given set of genes.