BOL: Related items

CLA: Contig-Layout-Authenticator

Jit — Fri, 05 May 2017 05:58:36 -0500

To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

Script https://sourceforge.net/projects/c-l-authenticator/files/

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155459

Computational Proteomics : Lets remember the basics

Jitendra Narayan — Thu, 01 Aug 2013 17:24:20 -0500

I spend some of my valuable time in computational drug designing sector. I remember my initial proteomics days, playing with interactive protein visualization software and dreaming big. Fortunately or unfortunately, I switched to genomics and handling the genomic floods in Petabytes which is expected to be in Brontobytes in coming years. Did I mention Brontobytes ??? Let me call to my server personnel … it gonna tsunami !!!!!

Today, refreshing my old memories I decided to blog about the basic knowledge of biochemistry and computational proteomics skills, but after I found several article on internet saying exactly what I had wanted to say I thought I might as well just redirect BOL's blog readers there instead:

Here is the list of website and videos links which provide a good resource for you basic chemistry need:

http://tecreativ.blogspot.co.uk/2012/09/funny-shortcut-remember-periodic-table.html

This blog have some specific hindi word to remember entire periodic table. I really like

Group 14 (C Si Ge Sn Pb) -> Sentence “Chemistry Sir Gives Sanki Problems”

Sanki is a hindi word which mean crazy :P

I found this link useful as well http://www.wikihow.com/Memorise-the-Periodic-Table

The eagle genomics group provide an element of bioinformatics in periodic tables. Yes you got it, this is not periodic table rather bioinformatics tools with periodicals

http://elements.eaglegenomics.com/

You can also try this video links, which provide you an overview with tricks on periodic tables:

http://www.youtube.com/watch?v=fLSfgNxoVGk

http://www.youtube.com/user/periodicvideos

For drug design educational material, software, tools, databses, viewer, file format and many more stuff at one place http://www.allfordrugs.com/drug-design/ I highly recommend you all computational drug designer to bookmark this page for future studies as well.

I just remember one of my mini project in which I use my flash knowledge (flash .. oh ya flash) to explain amino acids in interactive and user friendly manner. I can’t provide It right now, but promise you to provide a link in near future. I hope that you will enjoy my flashy creative skills :).

Moreover, I found some of very interesting tricks to remember all amino acids chemical formulae on youtube at

http://www.youtube.com/watch?v=gqrWb0fmzQ&list=PL6132651E70BB5575

http://www.youtube.com/watch?v=C2GfoGXfySQ&list=PL6132651E70BB5575

Key points for computer added drug designers?
1. A shortage of biochemistry skills means that you absolutely nowhere in understanding the key concept and do research.
2. Keep handy with complex mathematical formula, before merely running tools or software.
3. Dig it better and deeper guys .. design it.

Bienko and Crosetto Labs

Fri, 12 May 2017 07:42:15 -0500

We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation to gene expression regulation. The Crosetto group engineers new molecular methods for single-cell and spatially resolved omic measurements of DNA, RNA, and proteins, with a strong focus on tumor heterogeneity. By sharing ideas and resources, we work synergistically towards a more quantitative understanding of life’s processes in healthy and diseased conditions.

https://bienkocrosettolabs.org/

Life of BI !!!

Jitendra Narayan — Thu, 22 Aug 2013 16:13:36 -0500

Hmm .. Don't worry you read it right .. this is not pi but bi ... "life of Bioinformatician(BI)".

Disclaimer: This cartoon is solely designed to create humour and fun, not to offend any PI, supervisor or student.

UK Genome Science Meeting, sept 2nd-4th, 2013

Poonam Mahapatra — Mon, 12 Aug 2013 12:03:21 -0500

Following the success of the last three years' UK Next Gen Sequencing meetings at Nottingham, the newly named UK Genome Science meeting aims to bring together experts from around the world to meet and discuss the current and future state of all aspects and applications of Next Generation Sequencing.

More at >> http://www.nottingham.ac.uk/deepseq/events.aspx

Personalised Medicine - Animation

Tue, 27 Aug 2013 10:07:24 -0500

Two animated case scenarios set now and in the future. These highlight potential differences in the way patients are treated now, and how they might be treated as healthcare becomes more tailored.

The 10th North East Bioinformatics Network (NEBINet) Annual Coordinators' Meet

Jit — Sat, 18 Nov 2017 15:02:44 -0600

The 10th North East Bioinformatics Network (NEBINet) Annual Coordinators' Meet organised by the Bioinformatics Centre, St Edmund's College, Shillong and sponsored by the Department of Biotechnology, Government of India, was held at St Edmund's College Auditorium here on Thursday. Meghalaya Governor Ganga Prasad graced the inaugural programme as chief guest.
In his inaugural address, the Governor said the panorama of scientific scenario has greatly changed over the years, the thrust areas have undergone a metamorphosis but the conceptual underpinning of the basic sciences still continues.
"Of late, the activity of basic research has been intricately intertwined with technology. And we are determined to carry forward this change, for it is through technology that science can actually reach the masses in our country and afar, and the changing times have also inculcated a culture of cross-departmental and interdisciplinary research. Science and technology has always played a pivotal role in taking a nation towards greater heights by ways of innovations and inventions," he added.
Prasad also hoped that discussions, suggestions and sharing of innovative ideas during the two-day 10th NEBINet Annual Coordinators' Meet will open up new avenues to make substantial advancement in Biological Sciences which will provide a platform for proper and effective delivery mechanism for the common man.
During the inaugural function, Advisor of Department of Biotechnology Dr T Madhan Mohan gave an overview of the NEBINet and Bioinformatics programme.
President of Epygen Biotech FZ LLC, Dubai, UAE, Dr Debayan Ghosh, delivered the keynote address.
St Edmund's College governing body secretary Brother Simon Coelho and St Edmund's College Principal Dr Sylvanus Lamare also spoke during the function.

IMTECH Lab

Sun, 15 Sep 2013 09:41:04 -0500

Computer Aided Protein Structure Prediction; Identification of Vaccine
Candidates (T-Epitope prediction); Analysis of Nucleotide/Protein Sequences; Development of Web Server/

Software; Creation of Public Domain Resources in Biology
Present Status::

Developing prediction methods for gene, beta-turn, secondary structure and MHC-binding sites.
Area of Interest ::

Comparison of force field simulations. Analysis of DNA-protein interactions using molecular mechanics methods.Drug Target Identification using in silico biology.

More @ http://www.imtech.res.in/bic/index.php?option=com_content&view=article&id=65

PIs: http://www.imtech.res.in/bic/index.php?option=com_content&view=article&id=69

Bioinformatics tools developed for Oxford Nanopore data analysis !

biogeek — Wed, 27 Dec 2017 20:47:30 -0600

MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly. Generally, assemblers are based on several different types of algorithms, such as greedy, overlap-layout-consensus (OLC), de Bruijn graph (DBG), and string graph.

List of analysis tools developed for Oxford Nanopore data

BWA
Fast nanopore data tuned alignment tool
https://github.com/lh3/bwa

GraphMap
Mapper for long and error-prone reads
https://github.com/isovic/graphmap

LAST
Nanopore tuned alignment tool
http://last.cbrc.jp/

LINKS
Software tool for long read scaffolding
https://github.com/warrenlr/LINKS/

marginAlign
Tools to align nanopore reads to a reference
https://github.com/benedictpaten/marginAlign

minoTour
Real time analysis tools
http://minotour.nottingham.ac.uk/

nanoCORR
Error-correction tool for nanopore sequence data
https://github.com/jgurtowski/nanocorr

NanoOK
Software for nanopore data, quality and error profiles
https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

Nanopolish
Nanopore analysis and genome assembly software
https://github.com/jts/nanopolish

nanopore
Variant-detection tool for nanopore sequence data
https://github.com/mitenjain/nanopore

Nanocorrect
Error-correction tool for nanopore sequence data
https://github.com/jts/nanocorrect/

npReader
Real-time conversion and analysis of nanopore reads
https://github.com/mdcao/npReader

poRe
Tool for analyzing and visualizing nanopore data
https://sourceforge.net/p/rpore/wiki/Home/

PoreSeq
Error-correction and variant-calling software
https://github.com/tszalay/poreseq

Poretools
Nanopore sequence analysis and visualization software
https://github.com/arq5x/poretools

SSPACE-LongRead
Genome scaffolding tool
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread

SMIS
Genome scaffolding tool
https://sourceforge.net/projects/phusion2/files/smis/

List of assemblers for Oxford Nanopore MinION long reads

LQS
DALIGNER, Celera OLC Nanocorrect,
Nanopolish corrector
https://github.com/jts/nanopolish

PBcR
HGAP or BLASR, Celera OLC
PBcR corrector
http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
–
Canu
MHAP, Celera OLC
Canu corrector
https://github.com/marbl/canu

Falcon
String graph, Celera OLC
Falcon corrector
https://github.com/PacificBiosciences/falcon

Miniasm
OLC
https://github.com/lh3/miniasm

ra-integrate
OLC
https://github.com/mariokostelac/ra-integrate/

ALLPATHS-LG
de Bruijn graph
ALLPATHS-L corrector
https://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12

SPAdes
de Bruijn graph
SPAdes corrector
http://bioinf.spbau.ru/spades

What is the objective of BINC examination?

Neel — Mon, 12 Aug 2013 09:36:53 -0500

I personally did not understand the objective behind BINC examination. Is government only try to show off that they are doing something to promote Indian bioinformatics sector?

Moreover, It looks like BINC indirectly putting an extra burden to bioinformatician, mentally and financially.