BOL: Related items

dotPlotly: Generate an interactive dot plot from mummer or minimap alignments

Rahul Nayak — Thu, 21 Feb 2019 10:22:17 -0600

Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Address of the bookmark: https://github.com/tpoorten/dotPlotly

shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams

Jit — Sat, 29 Feb 2020 00:39:50 -0600

shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package.

To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to the Single-genome plot menu.

To cretae two-genome plot for comparison of data across two genomes, go to the Two-genome plot menu.

For the detail format of input data, check the Input data format submenu of the Help menu.

shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinyChromosome.ncpgr.cn, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome.

https://yimingyu.shinyapps.io/shinychromosome/

https://www.sciencedirect.com/science/article/pii/S1672022919301883

Address of the bookmark: https://yimingyu.shinyapps.io/shinychromosome/

World of Omics

Rahul Agarwal — Tue, 16 Jul 2013 17:11:48 -0500

How many variants of "omics" techniques presently in use ?

Research Associate (RA) at IOB

Mon, 05 May 2014 08:38:54 -0500

Applications are invited for a post of Research Associate (RA) or Senior Research Fellow (SRF) in the ICMR project on "Integrated Analysis of Multi-omics Data in Human Gliomas".

We are looking for a motivated candidate for handling proteomic and/or transcriptomic and other data with a strong background in bioinformatics tools and database development. The project will include identification of novel peptides from mass spectrometry-based proteomic data.

Familiarity with statistical tools or wet lab experience will be an added advantage. The position is open for immediate appointment and available for two years. The applicant will be appointed as Research Associate or Senior Research Fellow based on qualifications as detailed below:

Research Associate: Ph.D. in Biological Science or Bioinformatics with relevant publications in peer reviewed journals. Familiarity with bioinformatics tools, database development, programming skills and proteomic and/or other omics data analysis. Salary will be as per ICMR rules and guidelines.

Senior Research Fellow: M.Sc./B.Tech. in any branch of biology/ biotechnology/bioinformatics, with minimum 2 years of research experience (essential). Familiarity with bioinformatics tools, database development, programming skills and proteomic data analysis. Salary will be as per ICMR rules and guidelines.

Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: ravi@ibioinformatics.org on or before May 15th, 2014.

Contact:
Dr. Ravi Sirdeshmukh
Distinguished Scientist & Associate Director, IOB,
Principal Advisor MSMC/MSCTR

Advertisement: www.ibioinformatics.org/careers.php

MIRO : miRNA omics

Jit — Tue, 04 Oct 2016 14:50:48 -0500

The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

Japanese Multi Omics Reference Panel, jMorp

Rahul Agarwal — Fri, 22 Dec 2017 20:18:37 -0600

Japanese Multi Omics Reference Panel, jMorp, is a database of metabolome and proteome data in plasma obtained from volunteers in ToMMo. Metabolome data were measured by proton NMR and LC-MS, and proteome data were obtained by nanoLC-MS. We could measure several thousands of metabolites including the uncharacterized ones, and several hundreds of proteins until now.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkx978/4563306

Address of the bookmark: https://jmorp.megabank.tohoku.ac.jp/2017/compounds

Drawback of Exome Sequencing

Rahul Agarwal — Mon, 02 Jun 2014 05:46:43 -0500

Dr Eric Londin, Assistant Professor, Thomas Jefferson University, USA, stated that analysis of 44 exome datasets from four different testing kits showed that they missed a high proportion of clinically relevant regions in the 56 ACMG genes. "At least one gene in each exome method was missing more than 40 percent of disease-causing genetic variants, and we found that the worst-performing method missed more than 90 percent of such variants in four of the 56 genes," he says.

Source: http://www.eurekalert.org/pub_releases/2014-05/esoh-pco052914.php

2 PhD Position-Bioinformatics Austria

Sun, 09 Feb 2020 03:13:05 -0600

1 position as a University Assistant for 3 years, 30 hours per week, starting as
soon as possible, at the Institute of Biomedical Informatics at Graz University of
Technology

A position for a doctoral candidate is available in Leila Taher’s new lab at the Institute for
Biomedical Informatics at Graz University of Technology (Austria, https://www.bioinfo.tugraz.at).
We develop and apply regulatory genomics and systems biology approaches to analyze large
genomic datasets. Our long-term goal is to gain novel insights into the mechanisms and
evolution of differential gene expression

Link:
https://www.tugraz.at/fileadmin/user_upload/tugrazExternal/1565e0f6-6c94-4077-a118-f84bc91c4b07/Stellenausschreibung_Bioinfo_FWF_Jan2020_EN.pdf

BETSY: A new backward-chaining expert system for automated development of pipelines in Bioinformatics

Jit — Mon, 17 Dec 2018 18:46:51 -0600

The BETSY provides a command-line interface and available at https://github.com/jefftc/changlab. A user first searches in the knowledge base for desired output and then BETSY develops an initial workflow to produce that data which is later examined by the user. The user can optimize the parameters, the algorithm to preprocess the data, and normalize it depending on the task.

Currently, BETSY consists of modules required for the microarray and next-generation sequencing data [4] such as expression analysis, classification, peak calling, and visualization.

Address of the bookmark: https://github.com/jefftc/changlab

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/