Search Results for "java swing projects"

A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

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

Projects and applications developed from the lab of Yuval Kluger at the Pathology department at Yale

Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit

GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.

CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU....

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated...

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.

rNA is an aligner for short reads produced by Next Generation Sequencers

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

gfit creates an interface between computational models and experimental data and provides tools for their analysis

This is bionically project.

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!

DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).

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)

Opensource software projects for genetics and genomics from Sage Bionetworks.

TreeSoft is a collection of softwares that build or manipulate phylogenetic trees.

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f

IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

This project aims to develop various tools for artificial life and complex systems simulations: from the simulator itself to generic generation tools.