Search Results for "sandbox:/mnt/data/project_plan.pod" - Page 4
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Showing 891 open source projects for "sandbox:/mnt/data/project_plan.pod"
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Intelligent testing agents | Checksum.aiCoding agents write the code. Checksum runs it—continuously testing against real APIs, real data, real edge cases—before it ever reaches production.
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Enterprise Job Scheduling SoftwareManaging your sprawling data center and cloud with disparate native schedulers creates chaos. Achieve unparalleled control and efficiency over your entire IT environment with JAMS job orchestration tools. JAMS provides the singular, centralized platform required to overcome the complexities of disparate native schedulers. Automate, secure, and govern all your workloads, eliminating fragmented control, compliance risks, and operational bottlenecks. JAMS streamlines operations and ensures audit-ready history, transforming your enterprise automation with confidence and precision.
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. ... -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. 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... -
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Calis-p
Estimates delta13C of species in a microbiome from proteome data
Calis-p (The CALgary approach to ISotopes in proteomics) is a java application to estimate isotopic composition (e.g. delta13C or delta15N) of individual species in a microbial community from a proteomic dataset. Calis-p 2.0 handles both natural isotope abundances and data from labelling experiments such as stable isotope probing (SIP). It requires a mzIdent (or target spectrum match) and mzML files as the input and requires about 1 min per mzML file with 10 threads and needs <10 Gb of RAM. It has been tested with data from various nano liquid chromatography/Orbitrap platforms. For successful SIP, it is extremely sensitive, but requires the 13C fraction to remain below 10%. ... -
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The Kinetic Simulation Algorithm Ontology (KiSAO; http://co.mbine.org/standards/kisao) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs. Development of KiSAO has moved to https://github.com/SED-ML/KiSAO/.
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The Cloud Sales Acceleration PlatformStreamline and automate your cloud sales cycle, enhance operational efficiency, and capitalize on marketplace opportunities with the Clazar Cloud Sales Acceleration Platform.
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This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.
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bioweb
polyglot language framework to analyze genetic data
polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences -
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MANTI.pl / muda.pl
muda.pl - MQ unified data assembler
...It congregates information from 4 different MaxQuant output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt file - additional data is inferred from different other source files from the MaxQuant txt folder but the starting point for the data assembly is solely the modificationSpecificPeptides.txt file. Maybe also useful for normal proteomics purposes but this script is heavily optimized for protein neo-termini identification and validation. ... -
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sciNote
Open source electronic lab notebook (ELN) for scientists
sciNote is an open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place. sciNote is specifically designed for life science students, researchers, lab technicians and group leaders. -
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We are developing data standards and software tools that implement these standards to develop a systemic approach to modeling, capturing, analyzing and disseminating flow cytometry data.
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Secure User Management, Made Simple | FronteggFrontegg powers modern businesses with a user management platform that’s fast to deploy and built to scale. Embed SSO, multi-tenancy, and a customer-facing admin portal using robust SDKs and APIs – no complex setup required. Designed for the Product-Led Growth era, it simplifies setup, secures your users, and frees your team to innovate. From startups to enterprises, Frontegg delivers enterprise-grade tools at zero cost to start. Kick off today.
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Quadric
Application for simple base-2 binary to base-4 DNA-code conversion
Quadric is an opensource file converter created by the Jomcraft Network development team. In it's core functionality this small utility can transform base-2 binary files into base-4 DNA-coded human-legible ASCII-files. -
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
.... * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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IntEnz is the name for the Integrated relational Enzyme database. IntEnz contains data curated and approved by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).
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...MATS handles replicate RNA-Seq data from both paired and unpaired study design. More information can be found at http://rnaseq-mats.sourceforge.net.
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CBMPy
PySCeS Constraint Based Modelling
...CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. CBMPy supports user interaction via: - interactive console or as a library for advanced use - GUI, visual representation of the model, analysis methods - a SOAP based webAPI exposes high level functionality via web services -
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NOVA
Analysis and visualization of complexome profiling data.
...Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441 -
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FastaTools
Performs several operations to Fasta protein databases
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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LymPHOS2
LymPHOS2 Web-App
...Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. Proteomics 2014, 20, 2275-2279. DOI: 10.1002/pmic.20140012 -
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HyLiTE
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremely challenging, particularly on a whole-genome scale. ... -
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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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PBTK Optimizer
Application for optimization of parameters in PBTK models
...Other parameters can be determined through in-vitro experiments or through extrapolation using published equations. When it is impractical to use these methods to estimate a parameter, techniques can be used to optimize parameters so that model results best fit validation data. This tool was designed to optimize a user-specified list of parameters to a user-specified PBTK model. The user also controls validation data and optimization algorithms. In addition to optimized parameters, the tool outputs statistical information about the fit of the optimized model. -
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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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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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PPIXpress
specific protein interaction networks from transcript expression
...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 alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 .
