Open Source Java Bio-Informatics Software - Page 14

The Disease Simulation Framework (DiSiF) represents a spatial simulation environment for infectious viral disease spread. The framework currently embodies a very simple framework for simulation in 2D space with focus on SARS and the Common Flu.

DicomReader is a simple Java Dicom files decipher. It handles headers and images within as well; data (headers and pixel-value images) will be saved into ascii clear text files. A pgm version of the image files is also provided.

Digital Image toolkit

DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.

This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment.

This project contains a set of files (Perl, Java, and an R package) used to perform analysis of oligonucleotide signatures in metagenomes and genomes.

DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

Dogwood is an ontology-aware Distributed Annotation System (DAS) server framework for the integration of biological, biomedical and clinical data.

DrPangloss is a python implementation of a three operator genetic algorithm, complete with a java swing GUI for running the GA and visualising performance, generation by generation

Drug name recognition and normalisation/grounding to DrugBank ids and standard names. Package provides 2 taggers: 1. DrugTagger - CRF-based with DrugBank presence feature (see feature set for details). 2. DrugnameGazetteer - gazetteer/dictionary-based. Dictionary created from DrugBank.ca database. Both taggers include grounding/normalisation to DrugBank ids and standard names. Feature set: Word, Word-1, Word+1, Word-1_Word, Word_Word+1, DrugBankPresence, POS DrugBankPresence feature indicates the presence of the drug name in the DrugBank. Using CONLL-Evaluation: processed 32065 tokens with 3656 phrases; found: 3251 phrases; correct: 2786. accuracy: 95.25%; precision: 85.70%; recall: 76.20%; FB1: 80.67 Using GATE Corpus Benchmark: Strict: P: 0.65 R: 0.73 F1: 0.69 Lenient: P: 0.74 R: 0.84 F1: 0.78 The details of how to reproduce evaluation, see README. To use standalone version for tagging download DrugExtractionStandalone.tar.gz from Files.

This project develops a web-based (JSP) Fuzzy Rule-Based Expert System for analyzing ECG (electro cardio gram) signals & diagnosing Tachi-Arrhythmias. Proj. main blocks: inference engine, knowledgebase, KB editor, explanation, and feature extraction.

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)

The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations.

The goal of this project is to make a biologic pathway simulation / emulation application. The ultimate goal is to feed different file types to the application and configure a pathway and its behaviour.

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster data sets.

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.