BOL: Related items

Genome Simulation with SLiM and msprime

BioStar — Fri, 31 Jan 2025 12:47:43 -0600

Genome simulation is an essential tool in population genetics, enabling researchers to model evolutionary processes and study genetic variation. Two widely used simulation tools in this field are SLiM and msprime. While both serve different purposes, they can be used together with the slendr framework to compare simulation outputs effectively.

Overview of SLiM and msprime

SLiM: Forward Genetic Simulator

SLiM is a free, open-source tool designed for forward genetic simulations. It allows researchers to model complex evolutionary scenarios, including selection, recombination, and demographic events, making it particularly useful for studying adaptation and selection in populations.

Key Features of SLiM:

Simulates population evolution forward in time
Supports custom evolutionary models using an embedded scripting language
Allows modeling of spatial and ecological dynamics
Provides high flexibility and extensibility for user-defined scenarios
Available on GitHub as an open-source project

msprime: Ancestry and Mutation Simulator

msprime is an efficient, open-source tool that simulates ancestry and mutations using a coalescent framework. It is known for its high-speed performance and low memory requirements, making it a popular choice for large-scale genomic simulations.

Key Features of msprime:

Implements coalescent simulations for ancestry modeling
Efficiently simulates large population histories
Supports the addition of mutations to genealogies
Developed using an open-source community model
Often faster and more memory-efficient than alternative simulators

Using SLiM and msprime with slendr

Both SLiM and msprime can be integrated with slendr, a framework that facilitates structured population genetic simulations. This integration allows for seamless comparison of simulation outputs.

How They Work Together:

SLiM and msprime simulations can be analyzed within slendr.
The ts_read() function in slendr enables loading and comparing tree sequence outputs from both simulators.
This integration allows researchers to validate simulation results and gain deeper insights into evolutionary processes.

Performance Considerations

While SLiM offers powerful forward simulations with extensive customization, msprime is often preferred for its speed and memory efficiency when simulating ancestry and mutations. The choice between the two depends on the research goals:

For detailed evolutionary modeling with selection and recombination: Use SLiM.
For large-scale coalescent simulations with mutations: Use msprime.
For comparing different simulation models and their outputs: Use slendr to integrate SLiM and msprime results.

Conclusion

SLiM and msprime are valuable tools for genome simulation, each serving distinct but complementary purposes in population genetics research. By leveraging the strengths of both simulators with slendr, researchers can conduct robust and efficient evolutionary simulations, enhancing our understanding of genetic diversity and adaptation.

For more information, check out the official GitHub repositories for SLiM and msprime, and explore the slendr framework for streamlined simulation workflow

Project Fellow Bioinformatics at Central Drug Research Institute

Mon, 27 Apr 2015 20:15:45 -0500

Project Fellow (Bioinformatics)
Central Drug Research Institute
Address: Chattar Manzil, M.G.Road, Kaisarbagh
Postal Code: 226001
City: Lucknow
State: Uttar Pradesh
Pay Scale: Rs.16,000/- (fixed) p.m.
Educational Requirements: M.Sc. in Bioinformatics with 55% marks for Gen. & OBC and 50% marks for SC/ST candidates, Physically and Visually handicapped candidates
Experience Requirements: Experience in computer-assisted scientific research in the area of Drug Design including Bio- molecular modeling and simulation studies, Virtual screening, pharmacophore perception, QSAR etc. Familiarity with Linux/Unixbased computer systems and required to participate and contribute to the development and application of computational models for the design and discovery of novel molecules as inhibitors or chemical probes
Details will be available at: http://cdriindia.org/uploaded/advt_no01-2015.pdf

How To Apply: Eligible candidates required to report for the Interview at 9:00 A.M. sharp on 11-05-2015 (For Position Code No. 001 to 009) and 12-05-2015 (For Position Code No. 010 to 016). Candidates reporting after 10:00 A.M will not be allowed to attend the interview. Eligible candidates may appear before the Selection Committee for interview on the date and time mentioned above at CDRI, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow-226031. Eligible candidates must bring with them duly filled up application form (which can be downloaded from our website www.cdriindia.org), along with Original certificates as well as attested copies of certificates of examinations starting from matriculation, date of birth, caste certificate (in case of SC/ST/OBC) experience certificate, publication, if any and recent passport size photograph etc. Original documents are essential for verification of the particulars quoted by the candidate in the application form and candidate failed to produce original documents at the time of verification, shall not be allowed to attend the interview. Any request for relaxation in this regard shall not be entertained.
Detail of Interview: 11-05-2015
Age Limit: 28 Years

Integrated mRNA and microRNA transcriptome analysis in Strand NGS

Strand — Tue, 04 Aug 2015 05:04:46 -0500

Using a nasopharyngeal carcinoma case study, this paper highlights the integrated transcriptome analysis capabilities of Strand NGS demonstrating the identification of miRNA – mRNA interactions in regulatory networks.
Read the application note on Integrated mRNA and microRNA transcriptome analysis in Strand NGS by Veena Hedatale and Rohit Gupta. For more information, please contact us

School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Project

Wed, 29 Apr 2015 21:26:19 -0500

School of Life Sciences, Jawaharlal Nehru University has issued notification dated 27.04.2015 to fill the vacancy of JRF / SRF / RA in CSIR funded Projec entitled "Structural and functional characterization of serine biosynthetic pathway enzymes from entamoeba histolytica". It is good chance to get job with IITKGP and brighten your future. Learn eligibility criteria and apply on or before 08.05.2015.

Employer: Jawaharlal Nehru University
Address: Dr. S. Gourinath, Principal Investigator, School Of Life Sciences, Jawaharlal Nehru University, New Delhi-110067
Email: not mentioned / provided for this job post
URL: http://www.jnu.ac.in/Career/currentjobs.htm
Phone: 011 2674 2575
Skills: not mentioned / required for this job post
Experience: Experience in molecular biology, structural biology and bioinformatics is desired
Education: M.Sc. in any field of life sciences.
Job Location: New Delhi, Delhi, India (View Jobs in New Delhi, Jobs in Delhi, Jobs in India)

Job Description: School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Projec

Name of the Post: JRF / SRF / RA

Salary: As per rules

Required Job Profile:

Candidate must possess M.Sc. in any field of life sciences.

Desired Job Profile:

Candidate having NET - CSIR or UGC and experience in molecular biology, structural biology and bioinformatics is desired and experience with publication is preferred.

How to apply:

Eligible and interested candidates should need to apply with complete details to the above mentioned address on or before 08.05.2015.

Refer to http://www.jnu.ac.in/Career/currentjobs.htm

Japanese Multi Omics Reference Panel, jMorp

Rahul Agarwal — Fri, 22 Dec 2017 20:18:37 -0600

Japanese Multi Omics Reference Panel, jMorp, is a database of metabolome and proteome data in plasma obtained from volunteers in ToMMo. Metabolome data were measured by proton NMR and LC-MS, and proteome data were obtained by nanoLC-MS. We could measure several thousands of metabolites including the uncharacterized ones, and several hundreds of proteins until now.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkx978/4563306

Address of the bookmark: https://jmorp.megabank.tohoku.ac.jp/2017/compounds

Research Fellows at AIMSCS, Hyderabad

Wed, 06 May 2015 06:23:33 -0500

C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS) - Hyderabad, Andhra Pradesh
Advertisement No.: 5/2015

Research Fellows Systems Biology job vacancy in C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS)

JRF : Qualification - M. Sc in Bioinformatics, Systems Biology, M. Sc statistics, or M. Tech in Bioinformatics,

Pay Scale : Rs. 25,000

SRF : Qualification- Qualification prescribed for JRF with 2 years of research experience.

Pay Scale : Rs. 28,000*

No.of Post: 2

Desirable: Candidates should have strong background in Computational biology, bioinformatics, statistics and algorithmic development. In addition to that previous experience of working on Linux, bio-informatics, NGS data analysis and Basic knowledge of biology is desirable. Programming on any one of the programming languages (C, C++, perl, python) and statistical framework (e.g. R, matlab, etc.) is highly desirable.

More at http://www.crraoaimscs.org/jrf_application_form_2015.pdf

2 PhD Position-Bioinformatics Austria

Sun, 09 Feb 2020 03:13:05 -0600

1 position as a University Assistant for 3 years, 30 hours per week, starting as
soon as possible, at the Institute of Biomedical Informatics at Graz University of
Technology

A position for a doctoral candidate is available in Leila Taher’s new lab at the Institute for
Biomedical Informatics at Graz University of Technology (Austria, https://www.bioinfo.tugraz.at).
We develop and apply regulatory genomics and systems biology approaches to analyze large
genomic datasets. Our long-term goal is to gain novel insights into the mechanisms and
evolution of differential gene expression

Link:
https://www.tugraz.at/fileadmin/user_upload/tugrazExternal/1565e0f6-6c94-4077-a118-f84bc91c4b07/Stellenausschreibung_Bioinfo_FWF_Jan2020_EN.pdf

Perl One liner basics !!

Abhimanyu Singh — Sun, 24 May 2015 09:28:33 -0500

Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:

$ perl -e 'print "Hello, World!\n"'
Hello, World!

It's important that you use single-quotes to quote the code for -e. This usually means you can't use single-quotes within the one liner code. If you're using Windows cmd.exe or PowerShell, you must use double-quotes instead.

I'm always forgetting what Perl's predefined special variables do, and often test them at the command line with a one liner to see what they contain. For instance do you remember what $^O is?

$ perl -e 'print "$^O\n"'
linux

It's the operating system name. With that cleared up, let's see what else we can do. If you're using a relatively new Perl (5.10.0 or higher) you can use the -E switch instead of -e. This turns on some of Perl's newer features, like say, which prints a string and appends a newline to it. This saves typing and makes the code cleaner:

$ perl -E 'say "$^O"'
linux

Pretty handy! say is a nifty feature that you'll use again and again.

Pathway Analysis

Rahul Agarwal — Fri, 03 Oct 2014 08:51:13 -0500

Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set of expressed genes follow but also to disclose the relationships between these genes. With availability of more genomics, transcriptomics and proteomics data, interactions between genes involve in multiple pathways become more clear and also relationships between the genes, their transcripts, and their gene products. However, existing tools and dbs mainly based on knowledge driven approach in which pathways will be identified by finding the correlation between the information in one of the pathway knowledge databases (KEGG,Reactome,Panther,BioCarta, Panther,GO,NCI,WikiPathways,etc) and gene expression result for a specific conditions for instance tumor, obesity , cold resistant crops/plants, etc.

Introductory Articles/ppt/sources:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375

http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/Pathway%20Analysis.pdf

http://gettinggeneticsdone.blogspot.de/2012/03/pathway-analysis-for-high-throughput.html

http://davetang.org/muse/tag/pathway/

https://www.biostars.org/p/42219/

http://bioinformatics.ca//files/public/Pathways_2014_Module4_v2.pdf

http://bioinformatics.ca//files/public/Pathways_2014_Module2.pdf

Impotant Database and Tools:

GeneMANIA, Cytoscape, IPA and Metacore (Commerical ), Pathway Commons, Reactome ,Panther, BioCyc, WikiPathways, Pathvisio, KEGG, NCI, Stringdb, Amigo, WebGestalt ,ConsensusPathDB ,GSEA,Blast2go

Popular R based tools:

Reactome.db, ReactomePA, ClusterProfiler, Gage, SPIA, topGO, Pathview,DOSE,GOStat

More:

http://www.bioconductor.org/help/search/index.html?q=Enrichment+analysis+

Ryan E. Mills Lab

Tue, 26 May 2015 09:29:24 -0500

Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested in analyzing complex regions of the genome that are not easily resolved through modern sequencing approaches and which may exhibit interesting mechanistic origins.

We are also interested in the large-scale integration of genomic, expression, methylation and proteomic data sets, as well as the application of whole genome sequence analysis in clinical diagnostics.

More at http://millslab.ccmb.med.umich.edu/index.html