Open Source Java Bio-Informatics Software - Page 25

PhenoFam is a web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.

PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen

PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.

The goal of Picklist Editor is to display and modify pick lists before spot picking (in proteomics).

PileLine (Pileup pipeLine) is a toolkit for efficient handling of genomic position (GP) files, produced by next-generation sequencing experiments. It is designed to be memory efficient by performing on-disk operations over sorted GP files.

This library aims to provide support for D-dimensional images in Java and to enable high-level implementation of algorithms in dimensionally-invariant manner. Major features: the dimensionality and the access to primitive data types are abstracted.

The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.

A tool to visualize, analyze and store genomic positioning data.

An Evolution Simulator of Single Cells in a Pond. This shows a crosssection of water with sun shining from above. A single cell is dropped in and has various genes. The cells multipy and evolve. See Files above for download and screenshot.

Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends). Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3.

Praxiteles is a cross-platform interactive visualization tool for comparative genome map data. It is particularly well-suited to viewing multiple related genomes or chromosome segments that have highly diverged gene content and order.

Web application providing analysis of biomedical relationships. Built using the Grails web application framework (http://grails.org/) with MySQL (http://www.mysql.com/) as a back-end datastore and utilizing R (http://www.r-project.org/) for statistical analysis. Developed by the Dana Farber Cancer Institute (http://compbio.dfci.harvard.edu/) and Entagen (http://www.entagen.com).

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.

PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).

A simple Java application for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.

ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.

Featurama, superceding ProbePicker, is a bioinformatics program used to generate short probes from large datasets for use in DNA microarray experiments. A new project, BioSap, will extend the functionality of featurama.

The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.

A Java adaptation of DNA patterns based on the article "Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters". by Ilie Guta (Java source code for DNA patterns)

A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand proteins' : 1. Secondary structures 2. Conformational arrangements 3. Surface interactions

This project provides software resources for creating solid models of proteins that can be printed on color 3D printers. The main focus is a java program that reads in a PDB file and produces a PLY format stick representation of the protein.

PANDA (Protein And Nucleotide Data Archive) unifies the archival of the sequences from Taxonomy,GenBank,RefSeq,UniProt,PDB,and PRF on a regular interval to build and maintain a Protein and Nucleotide data archive. This project is part of BRC project fund

The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays.

PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.