Open Source Java Bio-Informatics Software - Page 31

VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set of methods for computational spectroscopy.

Ontologies, which are made up by standardized and defined controlled vocabulary terms and their inter-relationships, are comprehensive and readily searchable repositories for knowledge in a given domain

This project is an interactive viewer for 3D virtual screening data.

Genetic variants alter cellular behavior in a variety of ways, changing biochemical properties of DNA, mRNA, and proteins. Many large-scale sequencing projects are under way to detect human variation in health and disease. Although broad disease associations can be discovered by GWAS studies, the low-level impact of mutations is hardly available in structured form. The results of thousands of small-scale experiments, on the other hand, are present in the literature and discuss observations made ranging from alteration of active sites to changes in drug response resulting. Our aim is to bridge the gap between detection of genetic variants and their annotation with aforementioned observations. VarImpact extracts experimentally observed changes from the literature. This allows to annotate sequencing results with observed impacts, gather information about the mutational landscape observed in disease populations, and to study disease mechanisms. Check our Wiki for more!

A plugin package for ImageJ that assists with quantification and characterization of vascular networks. The tool regularizes lighting, segments the vessels, and generates a skeletal description that reflects the biological structures of interest.

The objective of this project is to provide a graphical visualization for statistical epistasis.  Pairwise and three-way epistatic interactions are measured using information gain and are represented using networks.

This project and all source code has moved to GitHub, see https://github.com/virtualcell

virtualDNA is a Processing3 game with an Android APK file in it. You can make your own flowers by crossing a flowerpool. There is a gamelike feature where you have to make a flower that ressembles a given one.

Web-based Electronic Data Capture (EDC) software for clinical trials. Uses XML-based data store based on CDISC ODM standard for clinical data interchange.

An artificial life and cellular automata simulator, inspired by Conway's Game of Life.

WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.

WHATCH’EM simulates the highly non-linear manner in which atmospheric conditions and container characteristics determine water temperature and height, leading to results that are not always intuitive and likely not simulated by simpler empirical models. WHATCH’EM has the capacity to be utilized for other mosquitoes and other container-inhabiting arthropods.

The WISDOM project is a Grid based production environment used to deploy bio-informatics large scale applications.

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

Wavelets At Work is a graphical tool (written in java) using wavelets in order to detect discontinuity of an input signal.

Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)

Winnow is a graphical application for importing and organising articles from PubMed. It gives access to abstracts, full text and allows references to be saved. It can also predict what a user will find interesting through adaptive filtering.

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

WrapImaJ purposes to be a multi-platform wrapper for different Image Processing systems for: - using the Java programming language. The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. In it's current form, it only wraps basic functionalities of ImageJ. The developers of WrapImaJ intend the library to support compatibilty with the main imaging systems available in the Java language and broadly used in the field of life sciences.

XMAS supports a new kind of “sit forward” time series microarray analysis through visual interaction and interoperable operators. Domain knowledge is integrated directly into the system to aid users in their analysis.

XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.

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.

The YeastsIdentification is a Java based application for searching for unique DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).

Managing Medical Insults.

ZAE is a Zoomable multiple sequence Alignment Editor