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The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).
PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
GEAX is a Java application used to visualize and analyze cross-species gene expression microarray data.The program allows comparisons based on fold-change, p-value, quantile matching, or a combination of criteria.
TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
Everything you need to build production-ready agents and models. Access 200+ Google and third-party AI models and tools.
Gemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.
IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.
It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
Visualize chromatographic properties for peptides from replicate, multi-site HPLC-MRM Mass Spectrometry experiments. RT Viewer was developed to easily visualize and troubleshoot chromatographic properties of a study across multiple laboratories.
TreeViewJ is a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches, and add names to nodes. Collection dates can be mapped onto a timeline, and sorted.
The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows