<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39114?offset=30 https://bioinformaticsonline.com/bookmarks/view/44885/firecrawl-the-web-data-api-for-ai-turn-entire-websites-into-llm-ready-markdown-or-structured-data Thu, 28 Aug 2025 02:34:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44885/firecrawl-the-web-data-api-for-ai-turn-entire-websites-into-llm-ready-markdown-or-structured-data <![CDATA[Firecrawl: The Web Data API for AI - Turn entire websites into LLM-ready markdown or structured data]]> Firecrawl is an API service that takes a URL, crawls it, and converts it into clean markdown or structured data. We crawl all accessible subpages and give you clean data for each. No sitemap required. Check out our documentation.

Pst. hey, you, join our stargazers :)

 

Address of the bookmark: https://github.com/firecrawl/firecrawl

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl Tue, 26 Dec 2017 18:06:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl <![CDATA[Building Web UIs With Mojolicious Perl]]> Mojolicious is one of 3 leading web frameworks available in the perl ecosystem (along with Dancer and Catalyst) and by far my favorite.

Mojolicious aims to provide a complete web development experience. It thus has no hard dependencies, comes with a built-in development and production server and many other features one needs to build a web application. It's easy to install, has an applciation generator script and many plugins and extensions.

Libraries for developing Web applications

Address of the bookmark: https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web Fri, 31 May 2019 19:55:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web <![CDATA[Apollo: First instantaneous, collaborative genomic annotation editor available on the Web]]>
  • Apollo is a plug-in for the JBrowse Genome Viewer.
  • In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
  • History tracking with undo/redo functions is available.
  • Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
  • Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
  • Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
  • Users may access a ‘Recent Changes’ page.
  • Help page with Apollo specific content is available.

    • Address of the bookmark: http://genomearchitect.github.io/

    ]]>     Jit     https://bioinformaticsonline.com/videolist/watch/16685/webinar-blast-in-the-cloud Mon, 15 Sep 2014 17:29:32 -0500 https://bioinformaticsonline.com/videolist/watch/16685/webinar-blast-in-the-cloud <![CDATA[Webinar: BLAST in the Cloud]]> Presented July 30, 2014 and covering: an NCBI BLAST AMI at Amazon Web Services; introduction to AWS and setting up an instance; running command line BLAST and using the BLAST URL API via the AMI; and answers to attendee questions.]]> https://bioinformaticsonline.com/blog/view/43424/rest-api Mon, 04 Oct 2021 12:46:40 -0500 https://bioinformaticsonline.com/blog/view/43424/rest-api <![CDATA[REST API]]> REST API

    The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

    Language
    Download
    Requirements
    Perl psiblast.pl LWP and XML::Simple

    Python

    psiblast.py

    		 xmltramp2

    For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/40834/nucleus-python-and-c-code-for-reading-and-writing-genomics-data Sun, 02 Feb 2020 08:14:19 -0600 https://bioinformaticsonline.com/bookmarks/view/40834/nucleus-python-and-c-code-for-reading-and-writing-genomics-data <![CDATA[Nucleus: Python and C++ code for reading and writing genomics data.]]> Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework, as anywhere a genomics file is consumed or produced, a TensorFlow tfrecords file may be used instead.

    Address of the bookmark: https://github.com/google/nucleus

    ]]>     Jit     https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis Sat, 20 Mar 2021 00:28:51 -0500 https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis <![CDATA[List of bioinformatics packages for NGS analysis !]]> Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

    • Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
    • Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
    • Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
    • BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
    • Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
    • SeqAn – The modern C++ library for sequence analysis.
    ]]>     Rahul Nayak     https://bioinformaticsonline.com/bookmarks/view/32853/progressivecactus Thu, 18 May 2017 05:29:29 -0500 https://bioinformaticsonline.com/bookmarks/view/32853/progressivecactus <![CDATA[progressiveCactus]]> Progressive Cactus is a whole-genome alignment package.

    Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

    https://github.com/glennhickey/progressiveCactus

    Address of the bookmark: https://github.com/glennhickey/progressiveCactus

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data Fri, 29 Mar 2019 01:21:54 -0500 https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data <![CDATA[OMTools: a software package for visualizing and processing optical mapping data]]> OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.

    https://github.com/TF-Chan-Lab/OMTools

    Address of the bookmark: https://github.com/TF-Chan-Lab/OMTools

    ]]>     BioJoker     https://bioinformaticsonline.com/bookmarks/view/42017/gromacs-a-versatile-package-to-perform-molecular-dynamics Thu, 06 Aug 2020 22:40:38 -0500 https://bioinformaticsonline.com/bookmarks/view/42017/gromacs-a-versatile-package-to-perform-molecular-dynamics <![CDATA[GROMACS: a versatile package to perform molecular dynamics]]> GROMACS is a versatile package to perform molecular dynamics, i.e simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is able to work with many biochemical molecules like proteins, lipids and nucleic acids. The WeNMR GROMACS web portal combines the versatility of this molecular dynamics package with the calculation power of the eNMR grid. This will enable you to perform many simulations from the comfort of your internet browser anywhere in the world. The server is furthermore aimed to provide a user friendly and efficient MD experience by performing many preparation and optimization steps automatically.

    GROMACS conda https://bioconda.github.io/recipes/gromacs/README.html 

    Address of the bookmark: http://haddock.science.uu.nl/enmr/services/GROMACS/main.php

    ]]>     Neel