<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/28997?offset=310 https://bioinformaticsonline.com/bookmarks/view/29917/gojs Tue, 22 Nov 2016 08:25:37 -0600 https://bioinformaticsonline.com/bookmarks/view/29917/gojs <![CDATA[GoJS]]> GoJS is a feature-rich JavaScript library for implementing custom interactive diagrams and complex visualizations across modern web browsers and platforms. GoJS makes constructing JavaScript diagrams of complex nodes, links, and groups easy with customizable templates and layouts.

GoJS offers many advanced features for user interactivity such as drag-and-drop, copy-and-paste, in-place text editing, tooltips, context menus, automatic layouts, templates, data binding and models, transactional state and undo management, palettes, overviews, event handlers, commands, and an extensible tool system for custom operations.

GoJS is pure JavaScript, so users get interactivity without requiring round-trips to servers and without plugins. GoJS normally runs completely in the browser, rendering to an HTML5 Canvas element or SVG without any server-side requirements. GoJS does not depend on any JavaScript libraries or frameworks, so it should work with any HTML or JavaScript framework or with no framework at all.          

More at http://gojs.net/latest/index.html

Address of the bookmark: http://gojs.net/latest/index.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29995/hga Tue, 29 Nov 2016 07:25:53 -0600 https://bioinformaticsonline.com/bookmarks/view/29995/hga <![CDATA[HGA]]> HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler (Velvet or SPAdes in this version) and using a given kmer size. 3. Merging all the assemblies of the partition. 4. Combining all the assemblies of the partition (using velvet with kmer value of 31). 5. Finaly, re-assembling the whole dataset with the merged contigs or the combined contigs, using a given kmer size.

https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

Address of the bookmark: https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30557/speedseq Fri, 20 Jan 2017 06:05:43 -0600 https://bioinformaticsonline.com/bookmarks/view/30557/speedseq <![CDATA[SpeedSeq]]> A flexible framework for rapid genome analysis and interpretation

C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

Address of the bookmark: https://github.com/hall-lab/speedseq

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31526/sequenceserver Fri, 10 Mar 2017 08:51:55 -0600 https://bioinformaticsonline.com/bookmarks/view/31526/sequenceserver <![CDATA[sequenceserver]]> SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

More at http://sequenceserver.com.

Address of the bookmark: https://github.com/wurmlab/sequenceserver

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34862/pasa-gene-structure-annotation-and-analysis Tue, 26 Dec 2017 21:14:03 -0600 https://bioinformaticsonline.com/bookmarks/view/34862/pasa-gene-structure-annotation-and-analysis <![CDATA[PASA: Gene Structure Annotation and Analysis]]> PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Address of the bookmark: http://pasapipeline.github.io/

]]> biogeek https://bioinformaticsonline.com/bookmarks/view/34715/delta-a-new-web-based-3d-genome-visualization-and-analysis-platform Wed, 20 Dec 2017 08:49:55 -0600 https://bioinformaticsonline.com/bookmarks/view/34715/delta-a-new-web-based-3d-genome-visualization-and-analysis-platform <![CDATA[Delta: a new Web-based 3D genome visualization and analysis platform]]> Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Deltafeatures a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs.

https://github.com/zhangzhwlab/delta

Address of the bookmark: https://github.com/zhangzhwlab/delta

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35384/mgcv-the-microbial-genomic-context-viewer-for-comparative-genome-analysis Mon, 29 Jan 2018 04:55:46 -0600 https://bioinformaticsonline.com/bookmarks/view/35384/mgcv-the-microbial-genomic-context-viewer-for-comparative-genome-analysis <![CDATA[MGcV: the microbial genomic context viewer for comparative genome analysis]]> MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:

  1. Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
  2. Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36239/scilifelab-tutorial-for-bioinformatics-analysis Tue, 17 Apr 2018 04:33:00 -0500 https://bioinformaticsonline.com/bookmarks/view/36239/scilifelab-tutorial-for-bioinformatics-analysis <![CDATA[SciLifeLab tutorial for bioinformatics analysis !]]> SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.

Courses

Old courses (2012-2014)

Metagenomics Workshop

2015 November - Uppsala
2016 November - Uppsala
2017 November - Uppsala

Introduction to Bioinformatics Using NGS Data

2015 February - Uppsala 
2015 May - Gothenburg
2015 September - Uppsala
2015 November - Lund
2016 January - Uppsala
2016 April - Linköping
2016 September - Uppsala
2016 November - Umeå
2017 January - Uppsala
2017 May - Gothenburg
2017 September - Lund
2017 November - Uppsala
2018 February - Uppsala

Introduction to Genome Annotation

2015 April - Uppsala
2016 April - Uppsala
2017 April - Uppsala
2018 May - Uppsala

De Novo Genome Assembly

2016 November - Uppsala
2017 November - Uppsala

RNA-seq course

2015 October - Uppsala
2016 April - Uppsala
2016 October - Uppsala
2017 March - Uppsala
2017 November - Uppsala
RNAseq tutorials

R Programming Foundations for Life Scientists

2016 November - Uppsala
2017 Mars - Uppsala

Single cell RNA sequencing analysis

2017 October - Uppsala

Address of the bookmark: https://scilifelab.github.io/courses/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction Wed, 21 Feb 2024 06:19:41 -0600 https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction <![CDATA[pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction]]> ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

]]> LEGE https://bioinformaticsonline.com/pages/view/40226/bioinformatics-training-courses-at-rasa-lsi Wed, 06 Nov 2019 00:30:51 -0600 https://bioinformaticsonline.com/pages/view/40226/bioinformatics-training-courses-at-rasa-lsi <![CDATA[Bioinformatics Training Courses At RASA LSI]]> RASA conducts comprehensive Life Science skill development training courses in Pune, India for working professionals, researchers, students and job-seeker. The trainings are crafted meticulously, covering different modules of courses such as Bioinformatics course, In silico Drug Discovery course, Next Generation Sequence data analysis course, Molecular Biology & Life science software development course wherein you learn from industry leaders how to apply these skills in life science & have a command over software developing process  by using various methodologies. We conduct in-class training and instructor-led live online classes worldwide, along with corporate and skill development training worldwide.

Workshops are conducted in regular intervals on Drug Designing, Protein Modeling and Simulation, Chemoinformatics, Bioinformatics etc.The workshops are highly beneficial for working professionals, students, researcher for enhancements of the skills in short duration.

]]> RASA Life Sciences