Search Results for "run time java" - Page 2
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Showing 59 open source projects for "run time java"
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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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miRNA Temporal Analyzer (mirnaTA)
Differential expression analysis tool for miRNAs in temporal studies
The microRNA Temporal Analyzer (mirnaTA) is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies. It is implemented in Perl and R package (>= 2.13.0) and can be run across multiple platforms such as Linux, Mac and Windows. The mirnaTA requires that users provide data from a minimum of two time points and analyze up to 20 time points. To normalize data and remove technical variability, Normal Quantile Transformation (NQT) was used, and the normalized data is analyzed using linear regression model to locate any miRNAs which are differentially expressed in a linear manner. ... -
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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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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... -
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XNBC: neurobiology simulation tool
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site. -
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A next gen sequencing analysis pipeline designed to run on hadoop/hdfs written in java and PIG. For more info, contact Zack Ramjan at USC
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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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Seqshell
A JAVA GUI for performing the function of Tophat and Cuffdiff
Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email address when the job is done. (You will need to modify the source code to change the content to meet your special needs) Run-time information will be displayed in a JAVA output window. -
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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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MIDA
Mitochondiral Infectious Damage Adaptation (MIDA) model of aging
This project provides the source code for the Mitochondiral Infectious Damage Adaptation (MIDA) model of aging. A probabilistic modeling approach is applied by solving the master equation in mitochondrial quality state space in the presence of fusion-fission events, decay of functional quality, mitophagy and mitochondrial biogenesis, as well as molecular damage originating from a random source or from infectious events during fusion and fission. The provided source code is written in... -
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
...Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is written in Python3. 7.X is my rewrite in Java, but is still work in progress. Both are written to be as lightweight as possible so they can run with minimal memory-requirements on a desktop or laptop as well as on a compute cluster. If you have any problems with QUASR, please do contact me at the email address provided in the README. -
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
...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. -
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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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The creation of quantitative SBML models is a time-intensive manual process. Saint, an automated SBML annotation integration tool, aids the modeller and reduces development time by providing information about a model in an easy-to-use interface.
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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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RepeatMap is a collection of time/memory efficient algorithms and data structures to enable rapid counting & querying of kmers (sequences of length k) counts in large sequences. E.g. a query could be "how many times is 'ACGTCATGGTAC' found in a genome."
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Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.
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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.
