BOL: Related items

CRCRI Bioinfomatics Walk In on 08.10.2013

Fri, 27 Sep 2013 10:59:53 -0500

Walk-in-Interview for recruitment of one Project Fellow for a period of 10 months purely on temporary basis is proposed to be held at Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram for a KSCSTE funded project entitled “PARTICIPATORY DEVELOPMENT OF A WEB BASED USER FRIENDLY CASSAVA EXPERT SYSTEM”

Salary: Rs. 10,000/- per month.

Age limit: 35 for men and 40 for women & SC/ST.

Qualification: First class in M. Sc (Agriculture)/MCA/M.Sc (IT)/ M. Sc (Computer Application)/M.Sc (Bioinformatics)/M.Sc (Geoinformatics).

Desirable: Two years experience in web design and web programming.

Date & time of interview: 08.10.2013, 10 am

Interested candidates may appear for an interview at this institute along with their application in plain paper containing the following particulars viz. (1) Name (2) Father/Husband/Guardian’s Name (3) date of birth & age as on 01.10.2013 (4) Permanent address (5) Address for communication (6) Email address and Telephone No. with code (7) Qualification (8) National fellowship like ICAR/CSIR/UGC etc. if any (9) Whether SC/ST/OBC (10) Details of experience (Attested copies of degree certificate, proof of age, mark sheets). Original certificates should be produced for verification.

No TA/DA will be admissible to the candidates attending the test. The selected candidate will have to join immediately.

Advertisement: http://www.ctcri.org/careers/mithra_SRF.doc

Programming language to build synthetic DNA

Jit — Mon, 30 Sep 2013 16:37:24 -0500

A team led by Georg Seelig (http://homes.cs.washington.edu/~seelig/index.html) at University of Washington has developed a programming language for chemistry that it hopes will streamline efforts to design a network that can guide the behavior of chemical-reaction mixtures in the same way that embedded electronic controllers guide cars, robots and other devices. In medicine, such networks could serve as “smart” drug deliverers or disease detectors at the cellular level.

Reference & More @

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html

http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/

Image source: washington.edu

Research assistant in computational biology

Wed, 24 Jun 2015 07:55:16 -0500

http://www.au.dk/en/about/vacant-positions/scientific-positions/stillinger/Vacancy/show/743161/5283/

Qualifications:
MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.

Deadline
01.08.2015

Walk-in-Interview @ Indian Agricultural Statistics Research Institute

Wed, 02 Oct 2013 15:40:17 -0500

Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi – 110012

Walk-in-Interview

Walk-in-interview will be held on October 5, 2013 at 10:00 A.M. at IASRI, New Delhi for a project “A New Distributed Computing Framework for Data Mining” funded by Department of Electronics and Information Technology, Government of India for the following posts. The appointment will be on contractual basis upto 14th October, 2015 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.

Research Associate

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or

Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 1st Division and at least two years of research experience

 Knowledge of Statistical Analysis /Bioinformatics tools for computational genomics.

 Knowledge of R/Perl programming language

Research Associate

Ph.D. in Computer Science/ Computer Application / Bioinformatics/ Agricultural
Statistics/ Statistics or equivalent or

Post-Graduation in Computer Science/ Computer Application /Bioinformatics/ Agricultural Statistics/ Statistics or equivalent with 1st Division and at least two years of research experience

 Expertise in Java programming.
 Knowledge of system administration and networking under Linux environment.
 Knowledge of parallel programming and cluster computing.

Emoluments for Research Associate: Consolidated Rs:24000/- per month + HRA (for Ph.D. Degree holders) and Rs:23000/- per month + HRA (for Master’s Degree holders)

Age Limit: Age should be not more than 40 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates as on date of interview).

Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph.

Original certificates/ Degrees are needed to be produced at the time of interview.

No T.A. /D.A. will be paid for appearing in the interview.

Advertisement: http://www.iasri.res.in/employment/employment.htm

Free resources to learn statistics

BioStar — Sat, 06 Jul 2024 10:30:50 -0500

Welcome to the course notes for STAT 414: Introduction to Probability Theory. These notes are designed and developed by Penn State's Department of Statistics and offered as open educational resources. These notes are free to use under Creative Commons license CC BY-NC 4.0.

A free online version of the second edition of the book based on Stat 110, Introduction to Probability by Joe Blitzstein and Jessica Hwang, is now available at http://probabilitybook.net

Print copies are available via CRC Press, Amazon, and elsewhere.

Stat110x is also available as an edX course. Free signup at https://www.edx.org/course/introduction-to-probability-0

The edX course focuses on animations, interactive features, readings, and problem-solving, and is complementary to the Stat 110 lecture videos on YouTube, which are available at https://goo.gl/i7njSb

The Stat110x animations are available within the course and at https://goo.gl/g7pqTo

https://projects.iq.harvard.edu/stat110/home

Address of the bookmark: https://online.stat.psu.edu/stat414/

Run miniasm assembler on nanopore reads !

Jit — Mon, 18 Dec 2017 04:07:50 -0600

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.

Find the detail of the reads repeats:

fq2fa ONT_A.fastq ONT_A.fasta

minimap2 -xava-ont ONT_A.fasta ONT_A.fasta -t10 -X > AONT.paf

awk '{if($1==$6){print}}' AONT.paf > AONTself.paf

awk '$5=="-"' AONTself.paf | awk '{print $1}'| sort|uniq > invertedrepeat.list

Generated a few palindrome and repeats plots (highlighting only repeats largest than 10, 20 and 30 kb)

minidot -f 5 -m 30000 AONTself.paf > AONTself30000.eps
sed 's/_template_pass_FAH31515//' AONTself30000.eps > AONTself30000final.eps

minidot -f 5 -m 20000 AONTself.paf > AONTself20000.eps
sed 's/_template_pass_FAH31515//' AONTself20000.eps > AONTself20000final.eps

minidot -f 5 -m 10000 AONTself.paf > AONTself10000.eps
sed 's/_template_pass_FAH31515//' AONTself10000.eps > AONTself10000final.eps

Assemble with miniasm:

miniasm -f ONT_A.fasta AONT.paf > AONT.gfa
grep '^S' AONT.gfa |awk '{print ">"$2"\n"$3}' > AONT_miniasm.fasta

minimap2 -xasm10 AONT_miniasm.fasta AONT_miniasm.fasta -t1 -X > AONT_miniasm.paf

awk '{if($1==$6){print}}' AONT_miniasm.paf > AONT_miniasm_self.paf

minidot -f 5 -m 10000 AONT_miniasm_self.paf > AONT_miniasm_self10000.eps

Njoy the assembly !

Basic command-line to run BLAST

Shruti Paniwala — Wed, 14 Mar 2018 05:10:34 -0500

The goal of this tutorial is to run you through a demonstration of the command line, which you may not have seen or used much before.

All of the commands below can copy/pasted.

Install software

Copy and paste the following commands

sudo apt-get update && sudo apt-get -y install python ncbi-blast+

This updates the software list and installs the Python programming language and NCBI BLAST+.

Get Data

Grab some data to play with. Grab some cow and human RefSeq proteins:

wget ftp://ftp.ncbi.nih.gov/refseq/B_taurus/mRNA_Prot/cow.1.protein.faa.gz
wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.1.protein.faa.gz

This is only the first part of the human and cow protein files - there are 24 files total for human.

The database files are both gzipped, so lets unzip them

gunzip *gz
ls

Take a look at the head of each file:

head cow.1.protein.faa
head human.1.protein.faa

These are protein sequences in FASTA format. FASTA format is something many of you have probably seen in one form or another – it’s pretty ubiquitous. It’s just a text file, containing records; each record starts with a line beginning with a ‘>’, and then contains one or more lines of sequence text.

Note that the files are in fasta format, even though they end if ”.faa” instead of the usual ”.fasta”. This NCBI’s way of denoting that this is a fasta file with amino acids instead of nucleotides.

How many sequences are in each one?

grep -c '^>' cow.1.protein.faa
grep -c '^>' human.1.protein.faa

This grep command uses the c flag, which reports a count of lines with match to the pattern. In this case, the pattern is a regular expression, meaning match only lines that begin with a >.

This is a bit too big, lets take a smaller set for practice. Lets take the first two sequences of the cow proteins, which we can see are on the first 6 lines

head -6 cow.1.protein.faa > cow.small.faa

BLAST

Now we can blast these two cow sequences against the set of human sequences. First, we need to tell blast about our database. BLAST needs to do some pre-work on the database file prior to searching. This helps to make the software work a lot faster. Because you installed your own version of the sotware, you need to tell the shell where the software is located. Use the full path and the makeblastdb command:

makeblastdb -in human.1.protein.faa -dbtype prot
ls

Note that this makes a lot of extra files, with the same name as the database plus new extensions (.pin, .psq, etc). To make blast work, these files, called index files, must be in the same directory as the fasta file.

blastp [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
[-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-version]

Now we can run the blast job. We will use blastp, which is appropriate for protein to protein comparisons.

blastp -query cow.small.faa -db human.1.protein.faa

This gives us a lot of information on the terminal screen. But this is difficult to save and use later - Blast also gives the option of saving the text to a file.

    blastp -query cow.small.faa -db human.1.protein.faa -out cow_vs_human_blast_results.txt
ls

Take a look at the results using less. Note that there can be more than one match between the query and the same subject. These are referred to as high-scoring segment pairs (HSPs).

less cow_vs_human_blast_results.txt

So how do you know about all the options, such as the flag to create an output file? Lets also take a look at the help pages. Unfortunately there are no man pages (those are usually reserved for shell commands, but some software authors will provide them as well), but there is a text help output

blastp -help

To scroll through slowly

blastp -help | less

To quit the less screen, press the q key.

Parameters of interest include the -evalue (Default is 10?!?) and the -outfmt

Lets filter for more statistically significant matches with a different output format:

blastp \
-query cow.small.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 7

I broke the long single command into many lines with by “escaping” the newline. That forward slash tells the command line “Wait, I’m not done yet!”. So it waits for the next line of the command before executing.

Check out the results with less.

Lets try a medium sized data set next

head -199 cow.1.protein.faa > cow.medium.faa

What size is this db?

grep -c '^>' cow.medium.faa

Lets run the blast again, but this time lets return only the best hit for each query.

blastp \
-query cow.medium.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 6 \
-max_target_seqs 1

Summary

Review:

command line programs such as blast use flags to get information about how and what to do
blast options can be found by typing blastp -help
break a command up over many lines by using `` to “escape” the new line

Blastn

blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-qcov_hsp_perc float_value] [-max_hsps int_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.7.0+

Bioinformatics @ TATA MEMORIAL CENTRE, NAVI MUMBAI

Mon, 28 Oct 2013 10:40:25 -0500

TATA MEMORIAL CENTRE
ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER
KHARGHAR, NAVI MUMBAI – 410210

No. ACTREC/Advt./ 72 /2013

WALK IN INTERVIEW

1. JRF*
Genome-wide RNAi screen with human pooled tyrosine kinase shRNA libraries in head and neck squamous call carcinoma (HNSCC) cell lines
DBT A/C No. 3071, Dr. Amit Dutt

2. JRF
IRB Project ACTREC Funds
Dr. Amit Dutt

3. RA
Defining the cancer genome of Head and Neck Squamous Cell Carcinoma (HNSCC) with SNP arrays and next generation sequencing technology
A/C No. 2895, Dr. Amit Dutt

Duration of the Project: One year from the date of appointment, or as and when project terminates.

Consolidated Salary: RA : Rs. 40,000/- p.m.
JRF* (DBT): Rs. 20,800/- p.m.
JRF: Rs. 16,000/- p.m.
Date & Time: 6th November, 2013, at 10.00 a.m.

Venue: Conference Room

Minimum Qualifications and Experience:

RA: The ideal applicant should have a PhD in a relevant field. He/she should have a strong computational biology background, with demonstrated experience in coding using Perl, Python, Java or C++. He/she should be familiar with working in unix enviromnent, devising computational algorithms for data analysis, statistical data analysis in R and matlab and database programming using MySQL. Hands on experience in analyzing high throughput data would be an added advantage.

JRF* (DBT project): M.Sc. in Life Sciences or M.Tech in Biotechnology with good academic record (Minimum of 60% aggregate). Valid UGC-CSIR/DBT/ICMR JRF qualification and laboratory experience in molecular biology. Previous experience in molecular biology and animal tissue culture with high throughput platforms and ability to work with a large team would be desirable.

JRF (ACTREC project): M.Sc. in Life Sciences or M.Tech in Biotechnology with good academic record (Minimum of 60% aggregate). Minimum 2 yrs experience in molecular biology and animal tissue culture with high throughput platforms and ability to work with a large team is essential.

*M.Sc. degree obtained after a one year course will not be considered.

Candidates fulfilling above requirements should send their application by e-mail to
‘careers.duttlab@gmail.com. in the format given below so as to reach on or before
4th November, 2013.

http://www.actrec.gov.in/data%20files/2013/AD-RA-JR-TECHN-6-NOV.pdf

PhD at University of Calgary

Fri, 27 Dec 2013 20:24:39 -0600

Institution/Company:
University of Calgary
Location:
Calgary, AB
Job Description:

Novel diagnostic platform for detection of Osteoarthritis

I invite applications from highly motivated individuals to join my laboratory as a PhD student in Systems Biology at the University of Calgary McCaig Institute for Bone and Joint Health. This project is aimed at characterizing the networks of physical (protein-protein) interactions underlying inflammatory processes in patients with Osteoarthritis and how this differs from patients with Rheumatoid Arthritis and normal individuals. This work will eventually lead to the development of a novel diagnostic platform for the non-invasive and accurate detection of early Osteoarthritis. The selected candidate will use state-of-the-art computational methodologies to systematically analyze proteomic data, and develop /implement new algorithms to identify protein and functional interaction networks from high throughput experimental data. The individual will also benefit by working closely with experts at the UofC and UofA through an AIHS Alberta Osteoarthritis Team Grant which includes experts from all pillars of health research. The candidate will also be supported to attend bioinformatics workshops and conferences to advance and disseminate their research.
Qualifications: The ideal candidate will have a Master’s degree in Computational Biology, Bioinformatics, or equivalent with strong background knowledge of the Biological Sciences, Biochemistry, and Microbiology. The individual should additionally have experience in handling high-throughput data sets as well as programming skills. The candidate will be registered as a PhD student in Dr. Krawetz’s laboratory, located in the new state-of-the-art Health Research Innovation Centre at the UofC. The individual will have strong verbal and written skills and the ability to work efficiently in a team environment.

In addition to the outstanding research opportunities available in this setting, students also enjoy the many cultural and sporting amenities provided in the city of Calgary, and can take advantage of the unparalleled skiing and hiking in the Rocky Mountains that are less than an hour away.

Candidates must be academically competitive and will be expected to apply for external funding. The stipend is $25,000/yr. For outstanding PhD students, internal top-up award opportunities are available on a competitive basis. If interested in joining the lab, please contact Dr. Krawetz directly at rkrawetz@ucalgary.ca and provide the following information:

- Short cover letter explaining your interest in the lab
- Resume
- Scanned copy of transcript or listing of course grades
- Names and contact information for two individuals who will be willing to provide letters of reference

EMBO practical Course on "Bioinformatics and Genomes Analyses" at Hellenic Pasteur Institute, Athens, Greece

Sat, 21 Dec 2013 10:00:24 -0600

The main objectives of this Practical Course are to strengthen skills
of PhD students and young researchers in the domain of Bioinformatics
and Genome Data Analyses on the use of advanced fundamental algorithms
and their applications in genome studies.

The course topics will include theoretical and practical aspects in:
- Genomes comparisons,
- Evolutionary analyses (orthologs, paralogs and ancestral genomes
inference),
- RNAseq and Next Generation Sequencing (including algorithms, methods
and sequence mapping tools, data analyses and applications).

The course programme will be centred on theoretical presentations
followed by practical sessions. Practical sessions in a Linux
environment will involve Unix shell and Perl scripting. Participants
are assumed to be familiar with this environment.

A series of lectures delivered by prominent scientists on recent hot
topics in genome (Viruses, Prokaryotes, Eukaryotes) studies will be
included in the programme and future research perspectives will be
highlighted.

The topics that will be included in the course programme are similar
to those included in previously organized courses:http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Ph.D students and Post-Doctoral
Researchers in Academic Institutions, with background in Mathematics,
Statistics, Biology or Computer Science and who are involved in
Bioinformatics and Genomes studies.

Selection of participants will be based on their background, running
research projects and on expressed motivations.
Selected students will have free accommodation and meals and are
expected to contribute with 200 euros and to pay for their travel
expenses.
All participants (students and invited speakers) will stay in the same
hotel.

Detailed indications are available on the course web site: http://events.embo.org/14-comparative-genomics/index.html

Candidates are advised to complete carefully the application form,
together with an abstract of at least one of their running projects, a
"one-page CV" and a personal Identity Picture (Photo).

The application deadline is March 14, 2014.

The organizers:
Menelaos Manoussakis, Hellenic Pasteur Institute, Athens, Greece.
Evdokia Karagouni, Hellenic Pasteur Institute, Athens - Greece.
Evie Melanitou, Institut Pasteur Paris - France.
Fredj Tekaia ( Institut Pasteur Paris France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html

Date: 5 – 17 May, 2014.
More at http://events.embo.org/14-comparative-genomics/index.html
will take place in the ,