Open Source Java Bio-Informatics Software - Page 15

EZMWeb is an open source web-based bioinformation integration and search system. Users can search the integrated enzyme information.It implements the analysis of correlation between different enzymes,gives its visualized results through java applet.

EasyCluster is a simple protein sequences clustering tool.

EcoloSim is a Simulation Framework for simple spatial models in biology and ecology, in Java. Typical problems are behavior of a herd of cattle, growth of microbe cells and other populations.

The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.

A framework for image analysis and data analysis, aimed towards microscopy and the needs of current research.

This is a bio-informatic project for finding enzyme. It is only free for academic and non-commercial users. Any commercial use should obtain our permission. Please contact wugang@ise.neu.edu.cn or ccdatabank@hotmail.com.

EuroPhenome - a database for Mouse phenotype data

This is a computer model to study Evo-devo. It is the software of a project described in PLoS Computational Biology.

EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.

Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.

A platform for the integration of deterministic and stochastic models, for the simulation of the integrated models and for interactive exploration of the model behaviour.

The project is moved to GitHub : https://github.com/bekisz/exreco/ Exreco is a agent based platform for the simulation and study of the Darwinian evolutionary process. It aims to support the exploration of genetically rooted phenomena like - aging (programmed cell death) - sexual and asexual reproduction - altruism of individuals - spread of diseases The typical way of using Exreco starts by defining the behavior of your replicators ( agents that can reproduce and evolve over time), and defining the environment of these replicators. If it is all done you can let it run observing what kind of genes prevail over time. The tool typically runs the same world (experiment scenario) over and over again to have a statistical understanding of the various replicator strategies.

A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition.

Face detection can be regarded as a more general case of face localization. In face localization, the task is to find the locations and sizes of a known number of faces (usually one). In face detection, one does not have this additional information. Face detection is mostly used along with facial recognition feature to extract faces out of an image or video feed and identify the faces against a set of stored images. This feature can be used for tracking prisoners, attendance and signing in to user accounts. The Viola - Jones Algorithm presents a novel face detection technique, we would implement this technique for face detection and then use eigen faces method to recognize the person in the image. Once recognized the person can easily sign in to any applications without the need of typing passwords or usernames.

Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file.

FindRelatives is a plugin for Cytoscape. It lets the user select a set of nodes and it would find the close relatives of the set of nodes.

FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases.

FoodDiary is an mobile app, that helps you, tracking what you have eaten in order to stay fit ;). A foodlist is available, that gets updated as often, as possible, and every user has the ability to add and correct data. An activity list is available in order to track, how many calories you have burned. There is also an biodata recording included, that helps tracking your personal goals.

FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

Frigg is an umbrella for all public GenomeView support tools

Client tools for the FuncNet protein function analysis platform: http://funcnet.eu/

This project is an implementation of an algorithm by J. Keijsper and R. Pendavingh. The goal of the algorithm is to construct a phylogenetic level-1-network that is consistent with a given set of quartets.