BOL: Related items

Powerful books for learning data analysis with R

LEGE — Tue, 28 May 2024 07:42:56 -0500

R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R today:

https://csgillespie.github.io/efficientR/

https://r-graphics.org/

https://rstudio-education.github.io/hopr/

https://r-pkgs.org/

https://r4ds.had.co.nz/

Address of the bookmark: https://r-graphics.org/

SERB Sponsored School in Evolutionary Biology 2019, 12–26 March 2019

Fri, 14 Dec 2018 18:25:07 -0600

Venue: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Jakkur,
Bengaluru 560 064

Evolution provides the overarching framework for organizing our understanding of biological phenomena at multiple structural levels and spatio-temporal scales. As such, evolutionary biology is more of a perspective or weltanschauung on the living world rather than a sub-discipline of biology. Unfortunately, despite the centrality of evolution to all thinking in biology, evolutionary biology remains neglected in the Indian context although research in many areas, not traditionally thought to be within the ambit of evolutionary biology, would greatly benefit from an evolutionary perspective.

The first school in evolutionary biology in the country, sponsored by SERB, will be conducted at the Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru. The school aims to provide participants with an introduction to the historical development of evolutionary thought and the various ecological, genetic and developmental aspects of the evolutionary process. The school will also provide an introduction to formal evolutionary theory and statistical methods for the analysis of evolutionary data.

Master’s/Ph.D. scholars, postdoctoral researchers and young faculty members in India may apply online on or before 31 December 2018 at http://school2019.serbevolschool.in, where additional details about the school can also be found. In case of any difficulty with the submission of applications, please e-mail Prof. T. N. C. Vidya, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, at tncvidya.lab@gmail.com.

Selected participants will be provided 3-tier AC train fare and local hospitality. There is no registration fee.

phyloXML: XML for evolutionary biology and comparative genomics

Jit — Wed, 29 Nov 2017 10:04:48 -0600

phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to extensible nature of XML itself and the provision of elements by phyloXML, extensibility as well as domain specific applications are ensured. The structure of phyloXML is described by XML Schema Definition (XSD) language.

Address of the bookmark: http://www.phyloxml.org/

JBrowse 2: a modular genome browser with views of synteny and structural variation

Abhi — Tue, 25 Apr 2023 20:58:52 -0500

igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
jb2-web - stock instance of jbrowse-web v1.7.5
jb1 - stock instance of jbrowse 1 v1.16.11
jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

Address of the bookmark: https://github.com/GMOD/jb2profile

ZENBU: a collaborative, omics data integration and interactive visualization system

BioJoker — Fri, 04 Jan 2019 13:35:26 -0600

ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.
Please check our documentation wiki for details on how to use the system, or check out some of the views above.

Address of the bookmark: http://fantom.gsc.riken.jp/zenbu/

MOSS: A System for Detecting Software Similarity

Jit — Sat, 09 Dec 2017 08:59:07 -0600

Moss (for a Measure Of Software Similarity) is an automatic system for determining the similarity of programs. To date, the main application of Moss has been in detecting plagiarism in programming classes. Since its development in 1994, Moss has been very effective in this role. The algorithm behind moss is a significant improvement over other cheating detection algorithms (at least, over those known to us).

Moss can currently analyze code written in the following languages:

C, C++, Java, C#, Python, Visual Basic, Javascript, FORTRAN, ML, Haskell, Lisp, Scheme, Pascal, Modula2, Ada, Perl, TCL, Matlab, VHDL, Verilog, Spice, MIPS assembly, a8086 assembly, a8086 assembly, MIPS assembly, HCL2.

Address of the bookmark: https://theory.stanford.edu/~aiken/moss/

Data Steward / Research & Development Specialist at at the Luxembourg Centre for Systems Biomedicine (LCSB)

Sun, 25 Oct 2020 22:36:38 -0500

Applications should be addressed online to: Prof. Dr. Reinhard Schneider, Head of the Bioinformatics Core Facility

For further information, please contact: Dr. Pinar Alper (pinar.alper@uni.lu)

Applications should be submitted online and include:

A detailed curriculum vitae
Cover letter mentioning the reference number
List of publications/software projects
Description of past experience and future interests
Names and addresses of three referees
Early application is highly encouraged, as the applications will be processed upon reception. Please apply ONLINE formally through the HR system. Applications by email will not be considered.

*gn=gender neutral.

More at https://recruitment.uni.lu/en/details.html?nPostingId=54616&nPostingTargetId=74219&id=QMUFK026203F3VBQB7V7VV4S8&LG=UK&mask=karriereseiten&sType=Social%20Recruiting

MetaPred2CS

Manisha Mishra — Fri, 03 Mar 2017 05:15:07 -0600

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs). The methods implemented in MetaPred2CS are 2 co-evolutionary methods: in-silico two hybrid (i2h) and mirror tree (MT) methods and 4 genomics context based methods: phylogenetic profiling (PP), gene fusion (GF), gene neighbourhood (GN) and and gene operon methods (GO).

http://metapred2cs.ibers.aber.ac.uk/

Address of the bookmark: https://github.com/martinjvickers/MetaPred2CS

Anvio

Shruti Paniwala — Thu, 16 Jun 2016 18:15:41 -0500

In a nutshell

Anvi’o is an analysis and visualization platform for ‘omics data.

Please find the methods paper here: https://peerj.com/articles/1319/

Anvi’o would not have been possible without the help of many people who directly or indirectly contributed to its development. Here is the acknowledgements section of our methods paper

An analysis and visualization platform for 'omics data http://merenlab.org/projects/anvio

Paper https://peerj.com/articles/1839/

Address of the bookmark: https://github.com/meren/anvio

Genome Workbench 2.10.7

Gudiya Pal — Fri, 01 Jul 2016 12:09:59 -0500

Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

BLAST Tool: added support for local custom BLAST databases
Graphical Sequence View: added log scaling option for graph tracks
Generic Table View: new tutorial added

Bug Fixes and Improvements

Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
Tree View: layout updated to better accommodate nodes of different sizes
Table Import Dialog (MacOS): fixed issue with table visibility
Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
Graphical Sequence View: fixed protein coloration methods
Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
Search View: ORF Finder – fixed incorrect protein lengths
Fixed bug with not opening project file (.gbp) on a click
Fixed issues in GVF import
Fixed BLAST Search tool against NCBI databases not working
Fixed tblastn (protein BLAST) not working in standalone mode
Fixed GTF export failure