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Showing 55 open source projects for "order"
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1
relax
Molecular dynamics by NMR data analysis
...It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
2
Biological Pathway Exchange Language
A Data Exchange Format for Biological Pathway Information
...In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap. -
3
OpenClinic GA
Open Source Integrated Hospital Information Management System
OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities. OpenClinic GA and OpenClinic GMAO are owned by Frank Verbeke, MD, PhD at Post-Factum BV (https://www.post-factum.be) -
4
ParDRe
Parallel tool to remove duplicate DNA reads
...This tool will let the users to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset (e.g., assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. It is faster than multithreaded counterparts (end of 2015) for the same number of cores and, thanks to the message-passing technology, it can be executed on clusters. There also exists a MapReduce counterpart of ParDRe, called MarDRe (see the link above). UPDATE: From version 2.0.5 ParDRe also provides support to remove only optical duplicates (and leave biologically interesting duplicates) as well as to work with compressed input/output with .gz format. -
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5
FullSSR
SSR detection and primer designing software
Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step. -
6
Lipid Reporter
Modifies csv files with a range of user defined filters.
** Updated for Windows 10** Lipid Reporter takes your plain old Progenesis QI search exports and allows you to manipulate them in a quick, safe, predictable way. Now with better support for Progenesis QI grouped output! Why muddle things up with Excel? Use Lipid Reporter instead. The supplied filters are all about Lipids. Add the category names, reject Ids that our outside of your favourite retention time range and lots more! This program is not produced by Nonlinear Dynamics... -
7
SBW (Systems Biology Workbench)
Framework for Systems Biology
...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. -
8
FusionCatcher
Somatic fusion-genes finder for RNA-seq data
...The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc. - to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes. -
9
PsPM
A matlab suite for Psycho-Physiological Modelling
...A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although this website will maintained to provide further releases, there will be no active development on the SVN repository. Thank you for your understanding and for using PsPM. -
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10
packeis
Check for selection of RNA secondary structure
PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons. -
11
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 distributed computing framework for scalable Big Data processing. ... -
12
Pipebar
A fast and accurate pipeline for DNA barcoding analysis.
Molecular analyses require the use of multiple bioinformatics tools. Here we proposed a pipeline for DNA chromatograms analysis of Sanger platform by open-source tools integration in order to reduce cost with standard commercial licences ensuring high quality, robustness with reduced time. Pipebar is a python application created to automatization of processing chromatogram trace files to high-quality DNA sequences for downstream analyses. -
13
mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
14
BOWS
Bioinformatics Open Web Services
...BOWS allows incorporation of several independent applications since programmers can install them in HPC clusters in any programming language. The lonely requirement is to write a script named “arrow” which calls BOWS back-end services periodically in order to check for new processes and their required parameters. If a new process is found, the “arrow” script should change the requisition status from waiting to running, run the process in the HPC cluster and, when the job is complete, call a BOWS back-end service to send the results. The results will then be available to the requestor. ... -
15
GPU3SNP
Exhaustive search for third order epistatic interactions using CUDA
GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction. It provides a list with the combinations that have higher Mutual Information, which is used as measure for interaction. It is parallelized using CUDA and can exploit several GPUs in the same node/system. -
16
GNomEx
A Genomic LIMS and Data Repository
...It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing, Affy and Agilent Microarrays, Sequenom MassArray and Bioanalyzer. GNomEx is a web application with a Flash client user interface and a Java backend that runs on Apache Tomcat. MySQL is used for the database, although any modern RDBMS can be used. -
17
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... -
18
ParDRR-MPI
Parallel Duplicate Read Remover with MPI
...This tool will let the users to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset (e.g., assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. It is faster than multithreaded counterparts (end of 2015) for the same number of cores and, thanks to the message-passing technology, it can be executed on clusters. -
19
Trowel - Sequencing Error Corrector
Error Correction Module for Illumina Sequencing Reads
Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers. This tool guarantees high accuracy and speed. This tool has been developed since 21. Jan. 2013 by Euncheon Lim in Prof. Dr. Detlef Weigel's Lab in Max-Planck Institute for Developmental Biology. First of all, you have to install the exact version of boost(>=1.53.0), google sparse hash(>=2.0.2), GCC(>=4.6), autoconf(=2.69), and automake(=1.13). -
20
parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
parSRA is a framework to execute short read aligners on compute clusters. It uses the following techniques in order to improve scalability: 1) a fast splitting of the input reads using the FUSE kernel module available in most of current Linux distributions; 2) a balanced on-demand distribution of the reads based on the shared locks of UPC++, an extension of C++ for parallel computing that follows the Partitioned Global Address Space (PGAS) paradigm. parSRA is portable as its configuration file allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner. -
21
RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a “map” of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative-proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal... -
22
Phobos Application
Software for recording rodents' behavior during behavioral tests
...Phobos provides the possibility to easily calculate all possible experimental parameters at once immediately after the evaluation of the fear/anxiety level of each animal. All extracted files can be readily combined to one in order for statistical analyses to be performed. If you use Phobos for your research, please cite: Telonis AG, Margarity M.Phobos: a novel software for recording rodents' behavior during the thigmotaxis and the elevated plus-maze test. Neurosci Lett (2015) doi: 10.1016/j.neulet.2015.05.045 Paper link: http://www.sciencedirect.com/science/article/pii/S0304394015004103 For support, questions or feedback: atelonis@users.sourceforge.net -
23
FoodDiary
FoodDiary is an app, that tracks what you have eaten.
FoodDiary is an mobile app, that helps you, tracking what you have eaten in order to stay fit ;). A foodlist is available, that gets updated as often, as possible, and every user has the ability to add and correct data. An activity list is available in order to track, how many calories you have burned. There is also an biodata recording included, that helps tracking your personal goals. -
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CIG-P
CIG-P is a simple yet flexible data visualization tool
CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. -
25
EducationalLCS
eLCS - Educational Learning Classifier System
...This eLCS package includes 5 different implementations of a basic LCS algorithm, as part of a 6 stage set of demos that will be paired with the first introductory LCS textbook. Each eLCS implementations (from demo 2 up to demo 6) progressively add major components of the entire LCS algorithm in order to illustrate how work, how they are coded, and what impact they have on how an LCS algorithm runs. The Demo 6 version of eLCS is most similar to the UCS algorithm. Each version only includes the minimum code needed to perform the functions they were designed for. This way users can start by examining the simplest version of the code and progress forward. ...
