Search Results for "https" - Page 4
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Showing 244 open source projects for "https"
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Easily Host LLMs and Web Apps on Cloud RunRun frontend and backend services, batch jobs, host LLMs, and queue processing workloads without the need to manage infrastructure. Cloud Run gives you on-demand GPU access for hosting LLMs and running real-time AI—with 5-second cold starts and automatic scale-to-zero so you only pay for actual usage. New customers get $300 in free credit to start.
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Ship AI Apps Faster with Vertex AIShip AI apps and features faster with Vertex AI—your end-to-end AI platform. Access Gemini 3 and 200+ foundation models, fine-tune for your needs, and deploy with enterprise-grade MLOps. Build chatbots, agents, or custom models. New customers get $300 in free credit.
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LMAP_S
Lightweight Multigene Alignment and Phylogeny eStimation
Emanuel Maldonado and Agostinho Antunes (2019) LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinformatics, 20:739. doi: https://doi.org/10.1186/s12859-019-3292-5 -
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...OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML.
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Cut Data Warehouse Costs up to 54% with BigQueryBigQuery delivers up to 54% lower TCO than cloud alternatives. Migrate from legacy or competing warehouses using free BigQuery Migration Service with automated SQL translation. Get serverless scale with no infrastructure to manage, compressed storage, and flexible pricing—pay per query or commit for deeper discounts. New customers get $300 in free credit.
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
...How to Cite: DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information Kai Cheng; Yusen Zhou; Sriram Neelamegham Glycobiology (2017) 27 (3): 200-205 Source code also available at: https://github.com/neel-lab/DrawGlycan-SNFGv2 Abstract & Full Text: https://doi.org/10.1093/glycob/cww115 -
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rRNAFinder
Fast ribosomal RNA detector and annotator
...The input rRNA gene sequences are searched against the downloaded and reformatted SILVA SSU and LSU databases using blastn. Please refer to the README.md file from rRNAFinder GitHub repository located at https://github.com/xiaoli-dong/rRNAFinder for instructions on configuring and running rRNAFinder -
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reditools
RNA editing detection by NGS data
...NGS technologies offer a unique opportunity to investigate RNA editing. REDItools are simple python scripts conceived to investigate RNA editing at large-scale. REDItools are now hosted at https://github.com/BioinfoUNIBA/REDItools -
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CompleXChange
differential analysis of combinatorial protein complexes
...With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
...Computer Methods and Programs in Biomedicine 143:159-169. 2017. DOI: http://dx.doi.org/10.1016/j.cmpb.2017.03.010 You can see more information about AntibiogramJ in https://sourceforge.net/p/antibiogramj/wiki/Home/ Several videos explaining the use of AntibiogramJ are available in https://sourceforge.net/p/antibiogramj/wiki/Videos/ AntibiogramJ includes now the EUCAST v.9.0. Please address any question or comment to joheras at gmail.com -
Run Any Workload on Compute Engine VMsCompute Engine delivers high-performance virtual machines for web apps, databases, containers, and AI workloads. Choose from general-purpose, compute-optimized, or GPU/TPU-accelerated machine types—or build custom VMs to match your exact specs. With live migration and automatic failover, your workloads stay online. New customers get $300 in free credits.
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variantkey
Binary files for variantkey
Binary files for the variantkey library: https://github.com/Genomicsplc/variantkey The binary files are generated using the script: https://github.com/Genomicsplc/variantkey/blob/master/resources/tools/vkhexbin.sh from the Human Variation Sets in VCF Format [National Library of Medicine (NLM)]: ftp://ftp.ncbi.nih.gov/snp/organisms/ -
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...In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. Other repositories: - https://github.com/jenetics/jenetics Maven: - https://mvnrepository.com/artifact/io.jenetics
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MPICorMat
Parallel tool to construct correlation similarity matrices
...This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of the first module of the RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). RMTGeneNet users can exchange this CCM module by MPICorMat, benefit from its fast computation to generate the similarity matrix, and then use the similarity matrix as input for the second module (RMM) to construct the final gene co-expression network. -
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Meraculous-2D
Eukaryotic Genome Assembler
...The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608 -
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PPICompare
detection of rewiring events in protein interaction networks
PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x. -
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
...MANTIS is developed and maintained by the Evolutionary Ecology of Infectious Disease (EEID) research group at the Department of Zoology, University of Oxford, UK. For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN ACCESS) At the moment, MANTIS is not available on CRAN. To build a source package of MANTIS, use the script buildPackage.R To install MANTIS use 'install.packages(file.tar.gz,type="src",repo=NULL)' To test use test_V3.3_code.R Contact the main author of the publication above for further details. ... -
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The Disease Ontology has moved to Github. New project page: https://github.com/DiseaseOntology Disease Ontology is a stuctured controlled vocabulary originally based upon and mapped to medical billing codes. The goal of this ontology is to create a comprehensive hierachical controlled vocabulary to represent subsumptive disease relationships.
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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
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MrBayes is a program for the Bayesian estimation of phylogeny. The project has been moved to GitHub: https://github.com/NBISweden/MrBayes
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...Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. PLoS ONE 13(2): e0192858. https://doi.org/10.1371/journal.pone.0192858
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pySBOL
SWIG-Python wrappers for libSBOL
pySBOL is a SWIG-Python wrapper around libSBOL, a module for reading, writing, and constructing genetic designs according to the standardized specifications of the Synthetic Biology Open Language (SBOL). This page provides binary installers for Windows operating system for Python 2.7 and 3.6. For installation instructions, visit: https://pysbol2.readthedocs.io/en/latest/installation.html For full documentation, visit: https://pysbol2.readthedocs.io/en/latest/index.html -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. ... -
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ASSA
MOVED TO https://github.com/vanya-antonov/assa
THE DEVELOPMENT AND DISTRIBUTION OF THIS PROJECT HAVE BEEN MOVED TO GITHUB: https://github.com/vanya-antonov/assa -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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aXonica
An installation package for freeware bioimaging tools
Download link: https://www.dropbox.com/s/jelbrho05m7yg8y/NeuroX_v.1.0.zip?dl=0 For Instructions Manual see Download section. -
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LOCUST
Custom Sequence Locus Typer
...Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240
