BOL: Related items

A guide for complete R beginners :- Installing R packages

Archana Malhotra — Tue, 24 Feb 2015 20:23:34 -0600

Part of the reason R has become so popular is the vast array of packages available at the cran and bioconductor repositories. In the last few years, the number of packages has grown exponentially!

This is a short post giving steps on how to actually install R packages. Let’s suppose you want to install the ggplot2 package. Well nothing could be easier. We just fire up an R shell and type:
> install.packages("ggplot2")

In theory the package should just install, however:

if you are using Linux and don’t have root access, this command won’t work.
you will be asked to select your local mirror, i.e. which server should you use to download the package.

Installing packages without root access

First, you need to designate a directory where you will store the downloaded packages. On my machine, I use the directory /data/Rpackages/ After creating a package directory, to install a package we use the command:
> install.packages("ggplot2", lib="/data/Rpackages/") > library(ggplot2, lib.loc="/data/Rpackages/")

It’s a bit of a pain having to type /data/Rpackages/ all the time. To avoid this burden, we create a file .Renviron in our home area, and add the line R_LIBS=/data/Rpackages/ to it. This means that whenever you start R, the directory /data/Rpackages/ is added to the list of places to look for R packages and so:

> install.packages("ggplot2") > library(ggplot2)

just works!

Setting the repository

Every time you install a R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, simply:

create a file .Rprofile in your home area.
Add the following piece of code to it:

cat(".Rprofile: Setting UK repositoryn") r = getOption("repos") # hard code the UK repo for CRAN r["CRAN"] = "http://cran.uk.r-project.org" options(repos = r) rm(r)

I found this tip in a stackoverflow answer .

jobTree based python wrapper to run the genome simulation tool suite Evolver

Jit — Fri, 08 Dec 2017 16:26:32 -0600

evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI)

Tue, 31 Mar 2015 20:45:14 -0500

Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI)

Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent. Desirable: Knowledge of Statistical and Computational Genomics/ Proteomics/ Bioinformatics OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience. Desirable:Expertise on use of various software/ tool.

No.of Post: 2

Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.

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

Interested candidates are invited to appear for Walk-In interview at Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi -110012, along with filled in application form , all the original certificates from matriculation onwards, Ph.D. or M.Sc. certificate (as the case may be) must be produced at the time of interview in either original or provisional, Bio-Data, attested copies of all experience certificates, testimonials etc., one passport size photograph and one set of the self-attested photocopies of all the required certificates from matriculation onwards and an attested copy of recent passport size photograph pasted onto the application form. Walk-in interview will be held on 16th April, 2015 at 10:30 a.m.

Click Here for Job Details & Application Form http://www.iasri.res.in/employment/employment.htm

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

List of universities offering Bachelor, Master or PhD bioinformatics degree in Malaysia

sahabuddin — Thu, 22 Jun 2017 01:34:02 -0500

Bioinformatics is a newly emerging interdisciplinary research area, which may be defined as the ―interface between biological and computational sciences. Most of the Bioinformatics work that is done can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. The global Bioinformatics industry has grown at a double-digit growth rate in the past and is expected to follow the same pattern in the next four years. US remains the largest market in the world, but Asia-Pacific countries, particularly India and China, are witnessing the fastest growth and are anticipated to emerge as the dominating forces in future. The Comparison of Bioinformatics Industry between Malaysia, India and other countries are discussed in this http://ijbssnet.com/journals/Vol.%202_No._10;_June_2011/11.pdf paper.

Bioinformatics is full of opportunities. The sector is poised to open new avenues for the other related sectors also. But the biggest opportunity area in the Bioinformatics market will be in the drug discovery sector. Reduction of both the cost and time taken to discover a new drug due to fast development in the Bioinformatics tools and software zone is also making drug discovery an attractive field to venture in. Malaysian bioinformatics growth and future are discuss in this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper. Keeping all such inportance in mind, following universities in Malaysia offering bioinformatics cources:

3 program(s) at AIMST University, Malaysia

Master of Science in Biotechnology (MSc) - Bioinformatics by Research

Master of Science (M.Sc) in Medical Microbiology (Bioinformatics) by Research

Doctor of Philosophy in Biotechnology (PhD) - Bioinformatics by Research

1 program(s) at INTI International University and Colleges, Malaysia

American Degree Transfer Program (Biosciences) in Bioinformatics

3 program(s) at Management and Science University (MSU), Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

1 program(s) at Multimedia University (MMU), Malaysia

Bachelor of Science (Honours) Bioinformatics

1 program(s) at Universiti Industri Selangor (UNISEL) Bestari Jaya Campus, Malaysia

Bachelor of Bioinformatics (Hons)

2 program(s) at Universiti Malaysia Sabah (UMS), Malaysia

PhD - Doctor of Philosophy in Bioinformatics (By Research)

MSc - Master of Science in Bioinformatics (By Research)

6 program(s) at Universiti Putra Malaysia (UPM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master of Science in Bioinformatics and System Biology by Research

Master of Science (M.Sc) in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics by Research

PhD - Doctor of Philosophy in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics and System Biology by Research

1 program(s) at Universiti Selangor (UNISEL), Malaysia

Bachelor of Bioinformatics (Hons)

3 program(s) at Universiti Teknologi Malaysia (UTM), Malaysia

M.Sc - Master of Science (Bioscience) in Bioinformatics Research Group (BIRG) By Research

PhD - Doctor of Philosophy (Bioscience) in Bioinformatics Research Group (BIRG) By Research

Bachelor of Computer Science (BioInformatics)

4 program(s) at University of Malaya (UM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master in Bioinformatics by Coursework

PhD - Doctor of Philosophy in Bioinformatics by Research

Bachelor of Science (BSc) in Bioinformatics

3 program(s) at Perdana University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

3 program(s) at Monash University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue. For detail Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges are discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

UIAR Short-Term Training/Final Year Dissertation Project in Life Sciences/Bioinformatics/Biotech

Mon, 16 Mar 2015 23:56:25 -0500

Short-term training/Final year dissertation project

Candidates desirous of doing a short-term training / final year dissertation project for MSc (Life Sciences/Bioinformatics/Biotechnology or any science discipline) at UIAR Biophysics and Bioinformatics department may please drop an email atanju@iiar.res.in along with their resume.

Selected candidates will be further intimated. There will be a fees charged for doing the project at UIAR. The projects will be experimental or computational or involve both.

The training scope will be in the following areas but not limited to:

Bioinformatics analysis, Docking and Virtual screening, Molecular Dynamics simulation, Cloning, expression and purification of proteins, Biophysical and Biochemical characterisation of proteins, Crystallization and Structural Studies.

Advertisement: www.iiar.res.in/?q=node/450

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Poonam Mahapatra — Mon, 04 Jun 2018 03:45:15 -0500

One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all

Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

Bioinformatics Engineer -- Algorithm Development

Wed, 01 Apr 2015 21:39:05 -0500

Centrillion Biosciences is a venture backed life sciences company located in Palo Alto, California. The company provides high quality genomic services to academic and industrial customers including top universities and research institutes. Centrillion Biosciences has an immediate opening for a full-time Bioinformatics Engineer. We're looking for an energetic, innovative, and motivated person who works well independently and on teams. The ideal candidate will have experience designing and implementing efficient algorithms to process large datasets. The role will involve collaborating with research scientists and other engineers, so strong communication skills are a must.

Job Description

• Work within a fast-paced, collaborative environment with small project teams working on a variety of tasks ranging from new product development to DNA data processing
• Collaborate with Centrillion research scientists in order to bridge the gap between the laboratory and the digital world
• Develop tools to enable research projects to cope with the enormous amounts of data produced by modern DNA sequencing experiments
• Build simulation algorithms to help guide and analyze research done in the lab
• Solve challenging engineering problems that require the development of innovative algorithms

Requirements

• Strong background in mathematics/statistics with a degree in a related field
• Strong analytical, coding, communication, and organizational skills
• Experience with algorithm development, simulations, and data analysis
• Proficiency in at least one modern programming language (like Python or Perl)
• Experience analyzing genetic and biological data sets (e.g., DNA data analysis and image analysis)
• Experience with machine learning and pattern recognition is preferred

Please submit your resume at https://www.centrillionbio.com/career/ to apply for this position.

SALSA: A tool to scaffold long read assemblies with Hi-C

Jit — Fri, 15 Jun 2018 04:01:15 -0500

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).

Address of the bookmark: https://github.com/machinegun/SALSA