Open Source Java Bio-Informatics Software - Page 3
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Java Bio-Informatics Software
View 66 business solutionsBrowse free open source Java Bio-Informatics Software and projects below. Use the toggles on the left to filter open source Java Bio-Informatics Software by OS, license, language, programming language, and project status.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Fully Managed MySQL, PostgreSQL, and SQL ServerCloud SQL handles your database ops end to end, so you can focus on your app.
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User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files
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TraceTuner
DNA sequencing quality values, base calling and trace processing
Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. Applied Biosystems SeqScape, Paracel Genome Assembler, MTexpert, etc.). -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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TreeGrOSS Forest Growth Simulation
Software for modelling tree growth
Tree Growth Open Source Software is a Java based version of the forest growth simulator for north west Germany BWINPro. -
Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
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The objective of this project is to make available an open-source version of our Multifactor Dimensionality Reduction (MDR) software. MDR is a nonparametric alternative to logistic regression for detecting and characterizing nonlinear interactions.
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PPIXpress
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 . -
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sRNAWorkbench
The UEA sRNA Workbench
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 -
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Go From AI Idea to AI App FastAccess Gemini 3 and 200+ models. Build chatbots, agents, or custom models with built-in monitoring and scaling.
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Entrainer is a Java program (JRE 1.8.0_40+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/". -
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[DEPRECATED] Gene Ontology
The DEPRECATED legacy location of the GO, see http://geneontology.org
The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads. -
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A tool for extracting and preprocessing spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP).
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. "GMOL: an interactive tool for 3D genome structure visualization." Scientific reports 6 (2016): 20802. -
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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PPICompare
detection of rewiring events in protein interaction networks
PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x. -
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PrimerSeq
Designs primers on flanking constitutive exons for RT-PCR
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SBW (Systems Biology Workbench)
Framework for Systems Biology
The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM. -
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TE-locate
a tool for calling transposons
TE-locate is a tool to locate all copies of sequences in a reference sequence using read-pairs. TE = Transposable Element Input is NGS-data. Please download all files first (including the demo data) and make your first run then. -
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VMS Draw
user-friendly access to the latest computational spectroscopy tools
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. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.
