{"id":367,"date":"2021-05-05T09:43:43","date_gmt":"2021-05-05T13:43:43","guid":{"rendered":"https:\/\/dev-gunsaluspiano.bio.nyu.edu\/?page_id=367"},"modified":"2025-03-28T15:00:19","modified_gmt":"2025-03-28T19:00:19","slug":"resources","status":"publish","type":"page","link":"https:\/\/gunsaluspiano.bio.nyu.edu\/?page_id=367","title":{"rendered":"Resources"},"content":{"rendered":"\t\t
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Resources<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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BioSAILS<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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BioSAILs (Bioinformatics Standardized Analysis Information Layers) is a scientific workflow management system (WMS) developed by the Core Bioinformatics Team at NYU Abu Dhabi (NYUAD; Rowe et al., 2019). It is the main engine running the analytical infrastructure at NYUAD, serving the Division of Biology and the NYUAD-CGSB. BioSAILs is open source software, available under the GNU license; the public Github project is available at Github \u2013 BioSAILs<\/a>, and HPC-Runner and BioX-Workflow can be installed through Conda using the BioConda channel. The BioSAILs web resource provides online documentation, support and guides, including blog posts related to analysis tasks using BioSAILs, forums, knowledge base and FAQs, as well as an interactive web-based workflow editor\/creator.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t

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NASQAR<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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NASQAR (Nucleic Acid SeQuence Analysis Resource)<\/a> is a web-based portal for high throughput data analysis and visualization developed by the NYUAD-CGSB Core Bioinformatics Team. This online resource provides an intuitive interface for researchers to easily upload, analyze, visualize, and explore their data interactively & effectively, using a collection of in-house developed apps and publicly available open source apps. The portal currently offers workflows for Data Preprocessing, RNAseq Analysis (Bulk and Single Cell transcriptomics with Seurat), and Metagenomics.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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Pheniqs<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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Pheniqs (Philology Encoder with Quality Statistics)<\/a> is a fast high-throughput sequencing read classifier implemented in multi threaded C++ that has been used by the NYU Center for Genomics and Systems Biology core facility since December 2014. It provides both a traditional Hamming distance-based barcode decoder and a more accurate maximum likelihood decoder that consults priors and quality scores. Pheniqs can read and write sequencing data from FASTQ, SAM, BAM and CRAM file formats and report the barcodes as well as decoding confidence for individual reads in SAM auxiliary tags. A flexible syntax enables Pheniqs to address reads at arbitrary offsets from both the 5\u2019 and 3\u2019 end and handle complex experimental designs that included sample, cellular and molecular barcodes. Using the maximum likelihood decoder, Pheniqs outperforms similar tools in speed, flexibility and accuracy.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t

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Rhevolution.org<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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Rhevolution.org<\/a> is a web archive describing and comparing early embryogenesis of 35 Rhabditidae<\/em> species. DIC movies spanning the one- to four-cell stages are systematically analyzed using a set of 40 binary phenotypic characters and are compared to C. elegans<\/em> embryogenesis.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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RNAi Database<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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RNAiDB<\/a> provides access to results from RNAi interference studies in C. elegans<\/em>, including images, movies, phenotypes, and graphical maps.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t

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Mouse Embryo Tracking<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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The Mouse Embryo Tracking Database<\/a> is a database and series of techniques related to the problem of tracking cells and detecting their divisions, in time-lapse movies of mammalian embryos.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

Resources BioSAILS BioSAILs (Bioinformatics Standardized Analysis Information Layers) is a scientific workflow management system (WMS) developed by the Core Bioinformatics Team at NYU Abu Dhabi (NYUAD; Rowe et al., 2019). It is the main engine running the analytical infrastructure at NYUAD, serving the Division of Biology and the NYUAD-CGSB. BioSAILs is open source software, available […]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":256,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-367","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/367","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=367"}],"version-history":[{"count":46,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/367\/revisions"}],"predecessor-version":[{"id":846,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/367\/revisions\/846"}],"up":[{"embeddable":true,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/256"}],"wp:attachment":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=367"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}