Search Results for "java time"
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Showing 28 open source projects for "java time"
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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GroIMP
Growth-grammar related Interactive Modelling Platform
Important: Groimp migrates to Gitlab. You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the... -
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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... -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2...
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spectralHMM
A spectral method for inferring selection from time series data
***WARNING*** This software was migrated to: https://github.com/popgenmethods/spectralHMM Support and updates will only be available at this new address. This software implements the algorithms described in the following paper: Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222 -
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Lab Inventory
Rediscover the Simplicity www.atgclabs.com
Request new Lab Inventory feature or module and receive a free Single User version with new feature. Help us to improve Lab Inventory. We want to hear your feedback! https://www.atgclabs.com/products/li The Lab Inventory System is an innovative, easy to learn solution for research laboratories. You can quickly and easily upload your existing Excel based inventory and get started in minutes, manage laboratory inventory, place orders and keep track of them in one place. Lab Inventory... -
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Sample Tracking
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Lab Storage
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available... -
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Exreco
EXperimental REplicator COllider
The project is moved to GitHub : https://github.com/bekisz/exreco/ Exreco is a agent based platform for the simulation and study of the Darwinian evolutionary process. It aims to support the exploration of genetically rooted phenomena like - aging (programmed cell death) - sexual and asexual reproduction - altruism of individuals - spread of diseases The typical way of using Exreco starts by defining the behavior of your replicators ( agents that can reproduce and evolve over... -
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Luscinia is a program for archiving and analyzing field sound recordings (especially of animals). It incorporates an interface to a database, spectrogram measurement algorithms, sound comparison algorithms, and statistical analysis.
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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xAffect
Sensor Middleware
xAffect is a software framework for online recording, processing and storage of multi sensor data. It was developed at FZI Research Center for Information Technology, Karlsruhe, Germany. xAffect can be used as a flexible, customizable middleware between physiological sensors and applications which require online feature computation (e.g. biofeedback or affective computing). Moreover, it can also be used as a standalone application for data acquisition and visualization. -
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DimerRemover
Remove adapter dimers from NGS data
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. -
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BioDare
BioDare is Biological Data Repository focused on timeseries data
BioDare (Biological Data Repository) was developed under the multi-site ROBuST project (http://hallidaylab.bio.ed.ac.uk/ROBuST.html) to support data exchange inside the project. It is a web application which allows data-sharing (including public dissemination), data-processing and analysis, with the main focus on time-series data produced in circadian experiments. The main features of BioDare are: - an online repository for experimental data accompanied by extensive... -
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GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.
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Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.
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sigTOOL provides a user-extendable signal analysis environment for processing electrophysiological data within MATLAB. Neuron spike-train, + spectral and time-domain analyses are built in. See http://dx.doi.org/10.1016/j.jneumeth.2008.11.004
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clinicalStudyTracker
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports. -
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BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.
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Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.
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A polynomial-time algorithm for constructing level-2 phylogenetic networks from dense sets of rooted triplets.
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SeEvolution is the first application that lets you see the effects of mutation events on 3D models of chromosomes. It takes you on a journey through time, showing you the changes that are necessary to go from the genome of an organism to another.
