Search Results for "java open source" - Page 35
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Showing 2101 open source projects for "java open source"
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Atera all-in-one platform IT management software with AI agentsAteraās AI agents donāt just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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CySBGN
Cytoscape plug-in that enables handling SBGN maps
CySBGN adds support to Cytoscape to import, export, visualize and analyse System Biology Graphical Notation (SBGN) maps. -
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simbTUM
Simulation of stochastic processes and ODE models in biology.
SIMulation of Biological systems (developed at the TU Munich) This program allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only). -
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SpiKeDeteKt
An automatic spike detection program to be used with new KlustaKwik
This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs... -
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HypoPhen
A hypocotyl phenotyping software
This is a semi-automatic high-throughput hypocotyl phenotyping software. It takes as input time-lapsed images of hypocotyls and measures their elongation and bending -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.
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Altrans
Quantification of Splicing Events
Altrans is a method for the relative quantification of splicing events. It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome. It uses paired end reads where one mate maps to one exon and the other mate to a different exon and/or split reads spanning exon exon junctions to count ālinksā between two exons. When there are overlapping exons, these are grouped into āexon groupsā and unique portions of... -
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Turn traffic into pipeline and prospects into customersDocket is an AI-powered sales enablement platform designed to unify go-to-market (GTM) data through its proprietary Sales Knowledge Lakeā¢ and activate it with intelligent AI agents. The platform helps marketing teams increase pipeline generation by 15% by engaging website visitors in human-like conversations and qualifying leads. For sales teams, Docket improves seller efficiency by 33% by providing instant product knowledge, retrieving collateral, and creating personalized documents. Built for GTM teams, Docket integrates with over 100 tools across the revenue tech stack and offers enterprise-grade security with SOC 2 Type II, GDPR, and ISO 27001 compliance. Customers report improved win rates, shorter sales cycles, and dramatically reduced response times. Docketās scalable, accurate, and fast AI agents deliver reliable answers with confidence scores, empowering teams to close deals faster.
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Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.
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SunlightCBM is a suite of perl scripts for constraint-based modelling and flux-balance analysis in metabolic networks.
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Dasty is a web client for visualizing protein sequence feature information using DAS, the Distributed Annotation System.
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NovelSeq
Novel sequence insertion detection
The NovelSeq pipeline is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. -
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Multiple Alignment Manipulator
MaM processes and manipulates multiple sequence alignments.
MaM is a software tool that processes and manipulates multiple alignments of genomic sequences. MaM computes the exact locations of common repeat elements in multiple aligned sequences, provided by a variety of user identified programs databases and tables. It then graphically displays how the alignment quality varies throughout the aligned sequences, providing separate displays for the repeat and non-repeat portions. -
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CUO
Codon Usage Optimizer
CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during the optimization process. ... -
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cancergrid-tma
A web-based application for the management of tissue microarray images
...The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis. -
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The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
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denovo_solid_pipeline
Pipeline for small genome assembly using SOLiD sequencing technology
denovo_solid_pipeline (DSP) is a semi automated pipeline for short genome assembly using SOLiD sequencing data. The main features of the pipeline are the optimization of the number of read-correction runs and computational resources via dynamic programming. DSP also has the advantage over the currently available pipeline (denovo2) of generating more contigs suitable for further assembly steps, increasing the chances of detecting sequencing errors and/or polymorphic sites. -
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Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
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SPA - SNP based pathway analysis
SNP based pathway analysis
Name: SPA Full name: SNP based pathway analysis Maintainer: jiangyongshuai@gmail.com liuguiyou1981@163.com Language: R package Description: SPA is an R package which can identify disease or phenotype related pathways. Input rs# and GWAS test p-values, you can get the related pathways. -
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birgHPCC
Rapid CUDA Cluster Deployment
birgHPCC is a major improvement over birgHPC (http://sourceforge.net/projects/birghpc/). While retaining the major functions of the original birgHPC, including automated computing cluster conversion and auto slots detection, the new version (birgHPCC) is capable of creating and configuring a compute unified device architecture (CUDA) computing cluster, hence the extra āCā in the name. In addition to the increase in image size (less than 2 gigabytes) and a new Linux base (previously Debian,... -
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve... -
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Xi Spectrum Viewer
Mass Spectrum Viewer Tool
To overcome current limitations in published MS data accessibility, we introduce a browser-based spectrum viewer that aims to allow exploration of alternative interpretations for MS spectra and additionally: can be operated by non-specialists, is open source, can be integrated into other software, gives appropriate publication-quality output. Spectrum Viewer is implemented totally on the client side using XHTML for menus and dialogs, SVG for spectrum and peptide display, and Javascript to drive functionality. It comprises 3 parts: (1) the core Spectrum Viewer displays peptide-spectrum matches and implements zooming, mouse-over peaks to highlight matching parts of peptide, mouse-over parts of peptide to highlight matching peaks, export SVG, and API; (2) the Auxiliary Annotator matches peptide to spectrum for given parameters and prepares the data for the Viewer; (3) these reside on a web page that provides the user control over peptides, spectra and other parameters e.g. linker mass.
