BOL: Related items

Nataša Pržulj Lab

Fri, 30 Aug 2013 06:29:17 -0500

Nataša Pržulj Lab's research involves applications of graph theory, mathematical modeling, and computational techniques to solving large-scale problems in computational and systems biology.They are interested in computational and theoretical solutions to practical problems in many areas of systems biology, planar cell polarity, proteomics, cancer informatics, and drug discovery and design.

More at http://www.doc.ic.ac.uk/~natasha/index.html

RA Bioinformatics at NII

Thu, 22 Oct 2015 01:56:26 -0500

NATIONAL INSTITUTE OF IMMUNOLOGY

NEW DELHI-110067

Applications are invited for the position of Research Associate (RA) for the following time-bound sponsored project as per the details given below:

1. BTIS project entitled, “National Infrastructural Facility in the Area of Immunology” funded by DBT

Research Associate (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: Ph.D in Bioinformatics or Biological Sciences or Biotechnology with research experience and publication record in indexed peer reviewed journals in the area of bioinformatics or computational biology.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience Research Associate: Rs. 36,000/- per month plus 30% HRA

Job description & Desired Knowledge: The candidate should be well versed in Programming in PERL/C++, HTML, CGI, web sever and portal development, computational analysis of protein structure & function, molecular dynamics simulations and use of high performance computing systems.

General Terms & Conditions:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.

2. No hostel/ housing facility will be provided.

3. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.

4. No TA/DA will be paid for attending the interview, if called for.

5. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise and list of publications. 6. Canvassing in any form will be a disqualification.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., Email ID, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC/ST/PH and Women candidates are exempted from payment of fees) subject to submission of documentary proof), at the time of interview. (E-MAIL APPLICATIONS SHOULD MENTION BTIS-RA 2015 IN THE SUBJECT LINE)

LAST DATE OF RECEIPT OF APPLICATIONS: 29th October, 2015

www1.nii.res.in/sites/default/files/projectappointments-Dr.Mohanty-29oct2015.pdf

The Minerva Research Group for Bioinformatics

Tue, 27 May 2014 15:48:14 -0500

The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

Perl Special Vars Quick Reference

Abhimanyu Singh — Tue, 07 Feb 2017 05:08:47 -0600

`$_`	The default or implicit variable.
`@_`	Subroutine parameters.
`$a` `$b`	sort comparison routine variables.
`@ARGV`	The command-line args.
Regular Expressions
`$`	Regexp parenthetical capture holders.
`$&`	Last successful match (degrades performance).
`${^MATCH}`	Similar to `$&` without performance penalty. Requires /p modifier.
$`	Prematch for last successful match string (degrades performance).
`${^PREMATCH}`	Similar to $` without performance penalty. Requires `/p` modifier.
`$'`	Postmatch for last successful match string (degrades performance).
`${^POSTMATCH}`	Similar to `$'` without performance penalty. Requires `/p` modifier.
`$+`	Last paren match.
`$^N`	Last closed paren match (last submatch).
`@+`	Offsets of ends of successful submatches in scope.
`@-`	Offsets of starts of successful submatches in scope.
`%+`	Like `@+`, but for named submatches.
`%-`	Like `@-`, but for named submatches.
`$^R`	Last regexp (?{code}) result.
`${^RE_DEBUG_FLAGS}`	Current value of regexp debugging flags. See `use re 'debug';`
`${^RE_TRIE_MAXBUF}`	Control memory allocations for RE optimizations for large alternations.
Encoding
`${^ENCODING}`	The object reference to the Encode object, used to convert the source code to Unicode.
`${^OPEN}`	Internal use: \0 separated Input / Output layer information.
`${^UNICODE}`	Read-only Unicode settings.
`${^UTF8CACHE}`	State of the internal UTF-8 offset caching code.
`${^UTF8LOCALE}`	Indicates whether UTF8 locale was detected at startup.
IO and Separators
`$.`	Current line number (or record number) of most recent filehandle.
`$/`	Input record separator.
`$\|`	Output autoflush. 1=autoflush, 0=default. Applies to currently selected handle.
`$,`	Output field separator (lists)
`$\`	Output record separator.
`$"`	Output list separator. (interpolated lists)
`$;`	Subscript separator. (Use a real multidimensional array instead.)
Formats
`$%`	Page number for currently selected output channel.
`$=`	Current page length.
`$-`	Number of lines left on page.
`$~`	Format name.
`$^`	Name of top-of-page format.
`$:`	Format line break characters
`$^L`	Form feed (default "\f").
`$^A`	Format Accumulator
Status Reporting
`$?`	Child error. Status code of most recent system call or pipe.
`$!`	Operating System Error. (What just went 'bang'?)
`%!`	Error number hash
`$^E`	Extended Operating System Error (Extra error explanation).
`$@`	Eval error.
`${^CHILD_ERROR_NATIVE}`	Native status returned by the last pipe close, backtick (`` ) command, successful call to wait() or waitpid(), or from the system() operator.
ID's and Process Information
`$$`	Process ID
`$<`	Real user id of process.
`$>`	Effective user id of process.
`$(`	Real group id of process.
`$)`	Effective group id of process.
`$0`	Program name.
`$^O`	Operating System name.
Perl Status Info
`$]`	Old: Version and patch number of perl interpreter. Deprecated.
`$^C`	Current value of flag associated with -c switch.
`$^D`	Current value of debugging flags
`$^F`	Maximum system file descriptor.
`$^I`	Value of the -i (inplace edit) switch.
`$^M`	Emergency Memory pool.
`$^P`	Internal variable for debugging support.
`$^R`	Last regexp (?{code}) result.
`$^S`	Exceptions being caught. (eval)
`$^T`	Base time of program start.
`$^V`	Perl version.
`$^W`	Status of -w switch
`${^WARNING_BITS}`	Current set of warning checks enabled by `use warnings;`
`$^X`	Perl executable name.
`${^GLOBAL_PHASE}`	Current phase of the Perl interpreter.
`$^H`	Internal use only: Hook into Lexical Scoping.
`%^H`	Internaluse only: Useful to implement scoped pragmas.
`${^TAINT}`	Taint mode read-only flag.
`${^WIN32_SLOPPY_STAT}`	If true on Windows `stat()` won't try to open the file.
Command Line Args
`ARGV`	Filehandle iterates over files from command line (see also `<>`).
`$ARGV`	Name of current file when reading <>
`@ARGV`	List of command line args.
`ARGVOUT`	Output filehandle for -i switch
Miscellaneous
`@F`	Autosplit (-a mode) recipient.
`@INC`	List of library paths.
`%INC`	Keys are filenames, values are paths to modules included via `use, require,` or `do`.
`%ENV`	Hash containing current environment variables
`%SIG`	Signal handlers.
`$[`	Array and substr first element (Deprecated!).

See perlvar for detailed descriptions of each of these (and a few more) special variables.

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Jit — Fri, 08 Dec 2017 16:48:40 -0600

Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to Tom Slezak for revsing the get_genbank_file3 script and to Tod Stuber (USDA) for testing version 3.1 even though he doesn't need the annotation feature. All users are encouraged to upgrade to version 3.1.

Address of the bookmark: https://sourceforge.net/projects/ksnp/files/

assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference genome

Jit — Thu, 14 Jun 2018 07:31:00 -0500

Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X faster) $ gzip OUT.delta Then use the OUT.delta.gz file for upload. Upload the .delta or delta.gz file (view example) to Assemblytics Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment. http://assemblytics.com/

Address of the bookmark: http://assemblytics.com/

Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism

Rahul Nayak — Sun, 23 Feb 2020 02:17:30 -0600

MCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples. To provide easy access to these sequences, we recently added a separate rRNA/ITS databases section on the nucleotide BLAST page for these targeted sequences that makes it convenient to quickly identify source organisms. The new databases are:

*16S ribosomal RNA (Bacteria and Archaea)

*18S ribosomal RNA sequences (SSU) from Fungi type and reference material

*28S ribosomal RNA sequences (LSU) from Fungi type and reference material

*Internal transcribed spacer region (ITS) from Fungi type and reference material

You can also download these from the BLAST db FTP area. See the NCBI Insights post for more detail.

Useful links

-----------------

BLAST form with rRNA/ITS databases

BLAST db download

Targeted loci

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

Internship program with ArrayGen Technolgies

Sun, 22 Jun 2014 23:18:31 -0500

Internship Program for Bioinformatics / Biotechnology Professionals Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

Interested candidates may email their resume along with a cover letter to careers@arraygen.com

Official website: http://www.arraygen.com/

The 8000 years old Tibetian gene mutation !!!

Neel — Wed, 20 Aug 2014 21:57:44 -0500

A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.

A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.

Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html

GrapheR !!!

John Parker — Thu, 14 Aug 2014 14:02:17 -0500

What a wonderful gem GrapheR is.... Oh yes it is. GrapheR is a GUI for base graphics in R by http://www.maximeherve.com/. The package provides a graphical user interface for creating base charts in R. It is ideal for beginners in R, as the user interface is very clear and the code is written along side into a text file, allowing users to recreate the charts directly in the console.

Adding and changing legends? Messing around with the plotting window settings? It is much easier/quicker with this GUI than reading the help file and trying to understand the various parameters.
Here is a little example using the iris data set.

library(GrapheR)
data(iris)
run.GrapheR()

This will bring up a window that helps me to create the chart and tweak the various parameters.

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!