Search Results for "check"
Sort By:
Showing 22 open source projects for "check"
View related business solutions-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
AI-generated apps that pass security reviewRetool lets you generate dashboards, admin panels, and workflows directly on your data. Type something like “Build me a revenue dashboard on my Stripe data” and get a working app with security, permissions, and compliance built in from day one. Whether on our cloud or self-hosted, create the internal software your team needs without compromising enterprise standards or control.
-
1
BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
...It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
2
123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ performs all the pre-processes of Illumina next-generation sequencing reads (FASTQ files) easier than ever. Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ,... -
3
SPiCEv2.1
Splicing Prediction in Consensus Element
...To access the tool's predictions, please use SPiP, accessible at : https://sourceforge.net/projects/splicing-prediction-pipeline/ or https://github.com/raphaelleman/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1.5 (05/2019) + corr (01/2020): Fix bug for linux version v2.1.4 (03/2019): Proxy management (only for Windows version) v2.1.3 (07/2018): correction bug for first 3' ss import vcf file v2.1.2 (06/2018): Import duplication Simplify import of deletion with one nucleotide Use tryCatch Improving web api connection check... -
4
MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
...MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php -
Fully Managed MySQL, PostgreSQL, and SQL ServerCloud SQL handles your database ops end to end, so you can focus on your app.
-
5
Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and makes extensive use of Numpy/Scipy. You can use any supported toolkit united under common API (for reference see Pybel or Cinfony). All methods and software based on Pybel/Cinfony should be drop-in compatible with ODDT toolkits. In contrast to its predecessors, which were aimed to have minimalistic API, ODDT introduces extended methods and... -
6
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. -
7
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. -
8
Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
-
9
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. BOWS is called from the front-end by Web Services, therefore a program running in a simple computer can benefit of high performance computation executed elsewhere. ... -
Gemini 3 and 200+ AI Models on One PlatformBuild generative AI apps with Vertex AI. Switch between models without switching platforms.
-
10
Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
-
11
SPANDx
Comparative analysis of haploid next-generation genome sequence data
...SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available. For the most up-to-date version of SPANDx, check us out on GitHub: https://github.com/dsarov/SPANDx -
12
...ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. ...
-
13
...Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out (August 2013): http://mbe.oxfordjournals.org/content/30/8.toc. For the multimodel version of CodonPhyML, please use the 'codonphyml_multi.tgz' tarball.
-
14
Create, check, annotate, merge, diff, split SBML (System Biology Markup Lanugage) documents. The latest version of semanticSBML is webbased with a RESTful interface.
-
15
mitoMaker
mitoMaker - a mitochondria pipeline wrapper script
...After various attempts to build different mitochondrial genomes in the lab I studied, a general pipeline started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters (mainly k-mer). Rinse and repeat until the best build is found. -
16
NIKS
NIKS (Needle in a K-stack) - detection of mutations in NGS data
To get access to the code, please check it out with svn as described in the code section. -
17
FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
...FineSplice requires Python 2.x (>= 2.6) with the following modules installed: pysam (http://code.google.com/p/pysam/) and scikit-learn (http://scikit-learn.org/). For further details check out our publication: Nucl. Acids Res. (2014) doi: 10.1093/nar/gku166 -
18
Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
-
19
RawGeno Version 2.0-1 is released! RawGeno is an R CRAN library automating the scoring of AFLP electropherograms. The library includes a graphical user interface to simplify its use. Note that the 2.0-1 version is delivered as a source (*.tar.gz for Linux and Mac users) and as a binary file (*.zip, for Windows users). The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy...
-
20
SeqWare has moved to GitHub, see https://github.com/SeqWare SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
-
21
It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
-
22
LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal. !!!!!! PROJECT MOVED TO GITHUB !!!!!! Please check out http://raphaelbauer.github.io/lajolla/
- Previous
- You're on page 1
- Next
