BOL: Related items

InfoGenomeR: Integrative reconstruction of cancer genome karyotypes

Jit — Wed, 05 May 2021 01:02:18 -0500

InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific CNAs, and haplotype information to identify the optimal breakpoint graph representing cancer genomes.

More at https://www.nature.com/articles/s41467-021-22671-6

Address of the bookmark: https://github.com/dmcblab/InfoGenomeR

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

Which are the best statistical programming languages to study for a bioinformatician?

Jitendra Narayan — Wed, 10 Jul 2013 14:35:34 -0500

In Bio-informatics based genome sequencing and predicting metabolic pathways research jobs I used Matlab, SAS, SPSS, R and several Bioconductor packages. Matlab had a lot of powerful tools and was easy to use, whereas SPSS is for non-programmers and R need programming skills. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

Smyth Lab

Sun, 14 Jul 2013 12:26:18 -0500

Statistical functional genomics in experimental medicine
The genome projects and the accelerated development of high-throughput genomic technologies such as microarrays have revolutionised biology. Making the most of this revolution requires the marriage of researchers from mathematical and biological backgrounds.

Research Area:
Linear models for microarray data
Digital gene expression technologies
Detection of molecular pathways
Bioinformatics resources for medical research

Link @ http://www.wehi.edu.au/faculty_members/professor_gordon_smyth/

Adhoc Bioinformatics Faculty Position @ NIT

Tue, 03 Jun 2014 16:19:52 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, DEPARTMENT OF BIOTECHNOLOGY, WARANGAL – 506 021, Andhra Pradesh

No.NITW/BT/2014/adhoc

APPLICATIONS ARE INVITED FOR THE APPOINTMENT OF ADHOC FACULTY ON CONTRACT BASIS IN THE DEAPARTMENT OF BIOTECHNOLOGY

Period of Contract: Initially the appointment is for one semester i.e., from July 2014 up to December 2014 only.

Essential Qualifications:

i) B. Tech or equivalent in Biotechnology/ Industrial Biotechnology/ Biochemical Engineering / Chemical Engg. Or M. Sc in Microbiology/ Botany/ Zoology/ Biochemistry/Biotechnology and ii) M. Tech or equivalent in Biotechnology/Industrial Biotechnology/Bioinformatics

Integrated M. Tech in Biotechnology/Industrial Biotechnology/ Bioinformatics

Candidates must possess First class (60% aggregate marks or 6.5 CGPA) at B. Tech/ M. Sc and M. Tech.

Desirable: Ph. D Pay Package: All selected candidates shall be eligible for a consolidated pay of Rs.30, 000/- per month. Candidates with Ph. D shall be eligible for an additional amount of Rs.5, 000/- per month.

How to apply : Applications on plain paper with attested photocopies of certificate and bio data along with justification for eligibility should reach to the Head, Department of Biotechnology, National Institute of Technology, Warangal AP 506004 in the form of soft or hard copy on or before 21st June 2014 email : biotech_hod@nitw.ac.in

Intimation: No separate call letters will be sent to the candidates. All the eligible candidates will be notified in the institute web site on 23rd June 2014. All the eligible candidates are requested to report for the interview to the Head, Department of Biotechnology at 9:00 AM on 27th June 2014

Joining: Selected candidates will be informed and they are expected to join immediately.

http://www.nitw.ac.in/nitw/announcements/2014/Bio-Adhoc%20Advt.%20May-2014.pdf

Livestock Functional Genomics Summer School (LFG 2013)

Fri, 02 Aug 2013 09:57:37 -0500

*Livestock Functional Genomics Summer School - Call for applications*

1st Livestock Functional Genomics Summer School (LFG 2013).

This School was designed for graduate students and early-stage researchers with interest in livestock genomics, who are engaged in projects that require knowledge in the field of computational biology.

Sixty selected participants will spend 13 days receiving theoretical and practical training in genomic data handling from internationally renowned experts.

After the course, the participant should understand the basis and the context of livestock big molecular data, and be able to manipulate high density genotypes, whole genome sequences and transcriptome data.

The Summer School will be held in Araçatuba-SP Brazil, from the 13th to the 21st of September 2013.

All accepted participants will have *expenses fully covered (air ticket, hotel and meals)*, including a free pass to the 5th International Symposium on Animal Functional Genomics http://www.isafg2013.org.br

Applicants will be selected based on their résumés. Application date is due by August 10th. Results will be announced in August 12th.

Please consult website: http://www.sciencesatellite.org.br/sschool

Search Shell Command History

Rahul Nayak — Thu, 12 Jun 2014 17:43:34 -0500

We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it?

Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c

The Human Genome Project Video 3D Animation Introduction Low)

Sat, 24 Aug 2013 19:01:19 -0500

Bioinformatician’s Pocket Reference !!

RAJESH DETROJA — Sun, 08 Jun 2014 09:56:58 -0500

It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core IT toolkits on their plate. It has become mandatory to be able to mould different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is best way to get syntax problem solved, it is not a bad idea to keep reference sheets is our smartphones or stick out some printed sheets on the back of your door, in the old fashion way!!

Address of the bookmark: http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/

Genome2014

Tue, 15 Oct 2013 12:47:32 -0500

Genomics has profoundly changed our way of conducting research in microbiology. The power of high–throughput DNA sequencing technologies, in particular the recent development of next generation sequencing allows researchers now to address an increasingly diverse range of biological problems. The scale and efficiency of sequence-based analyses that can now be achieved is providing unprecedented progress in diverse areas that range from the analyses of genomes to related disciplines such as transcriptional profiling - or protein - nucleic acid interaction studies: Population and metagenomics studies can now be conducted in an unprecedented large scale, regulatory processes can be studied genome-wide under hundreds of different conditions. The genome wide study of the interaction of DNA or RNA with proteins brings completely new insight into regulatory processes and even single cell analyses become now possible. The many diverse applications of next–generation sequencing and the importance of the insights that are being gained through these methods are very exiting and challenging. It is the perfect time to come together and exchange new knowledge and technologies in this area.

Thus the conference on "Microbiology after the genomics revolution - Genomes 2014" will be an appropriate and timely occasion to offer an outstanding discussion forum for the best international researchers in all fields of cutting edge microbiology research to discuss newly discovered aspects of microbiology.

More @ http://www.genomes-2014.org/