Search Results for "mysql-connector-java" - Page 3
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Showing 890 open source projects for "mysql-connector-java"
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BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format
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LymPHOS2
LymPHOS2 Web-App
LymPHOS2 is a web-based Application at www.LymPHOS.org containing peptidic and protein sequences and spectrometric information on the PhosphoProteome of human T-Lymphocytes. - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes... -
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Mass-Up
MALDI-TOF data analysis tool
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data. -
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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... -
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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer... -
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PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic... -
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@Note2
@Note2 - A workbench for Biomedical Text Mining
Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. -
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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.
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CompleXChange
differential analysis of combinatorial protein complexes
The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
AntibiogramJ is a Java program for the identification, measurement and categorisation of inhibition zones in antibiogram images captured with any device that incorporates a camera (including digital cameras and mobile phones). Citing AntibiogramJ: A. Alonso, C. Domínguez, J. Heras, E. Mata, V. Pascual, C. Torres, and M. Zarazaga. AntibiogramJ: a Tool for Analysing Images from Disk Diffusion Tests. -
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MarDRe
MapReduce-based tool to remove duplicate DNA reads
...Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. Written in pure Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for Big Data processing. -
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HSRA
Hadoop spliced read aligner for RNA-seq data
HSRA is a MapReduce-based parallel tool for mapping reads from RNA sequencing (RNA-seq) experiments. RNA-seq analyses typically begin by mapping reads to a reference genome in order to determine the location from which the reads were originated, which is a very time-consuming step. This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a... -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines... -
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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... -
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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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A genome wide mapping data interpretation platform for NGS(ChIPSeq). A tutorial can be found at: http://genomeast.igbmc.fr/wiki/doku.php?id=training:seqminer
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...Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. Other repositories: - https://github.com/jenetics/jenetics Maven: - https://mvnrepository.com/artifact/io.jenetics
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SMSD
SMSD is a Java based software library for calculating MCS.
SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure). -
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OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
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N2A
Neurons to Algorithms - A neural modeling and simulation workbench
"Neurons to Algorithms" (N2A) is a language for modeling neural systems, along with a software tool for editing models and simulating them. N2A is currently "alpha" software. The download provided on SF is for convenience to those who wish to preview the software. Please see our site on github for development status. -
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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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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
Raw genomic sequences are frequently contaminated with sequences of other organism. Their identification is essential for the interpretation of genomic data. In this context it is essential to distinguish between horizontal gene transfers and contamination. The genomic context of sequences can help distinguish the two scenarios. Taxoblast splits genomic scaffolds into sub-sequences of defined length and for each of them determines the closest related taxon. It then summarizes this...
