Department of Genetics

University of Delhi South Campus

NEW DELHI – 110 021

WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT & LAB / FIELD ATTENDANT

1 Research Scientist (RS) – 3

DBT, Ph. D.

Experience on DNA Markers, plant genome mapping and bioinformatics

Salary: 60,000 (Consolidated) + 5% annual increment

Date and time: 25.06.2015 at 10:30 AM

These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.

Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.

No TA/DA will be paid for attending the interview.

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3D-Dock Suite

Global rigid search: FFTShape complementarity and electrostatics

Re-scoring and clustering. Refinement of interface side-chains

3D-Garden

Global rigid search in ensamble

Shape complementarity and Lennard–Jones potential

Side chain and backbone dihedral refinement

DOT

Global rigid search: FFTShape complementarity, electrostatics and VDWNone

Escher NG

Global rigid searchShape complementarity, hydrogen bonds and electrostatic

Integrated in VEGA

GRAMM 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potential

Clustering of conformations

GRAMM-X 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potentialminimization and re-scoring with multiple filters

HEX

Global rigid search: Fourier correlation of spherical harmonics

Shape complementarity

HADDOCK

Global rigid searchElectrostatic ,VDW and desolvation energy termsMD simulated annealing refinement . Filtering based on external data. 

ICM

Global rigid search: Monte CarloEmpirical scoring function

Clustering and selection of conformations. Refinement of interface side-chains and re-scoring

MolFit 

Global rigid search: FFTShape complementarity

Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations

PatchDock

Global rigid searchShape complementarity and atomic desolvation energy

Clustering of conformations

PyDock

Global rigid search:FFTShape complementarity

rescoring by binding electrostatics and desolvation energy

RosettaDock

Local rigid search: Monte Carlo with low and high resolution structure representation levels

Different scoring parameters for the different resolutions 

ZDOCK

Global rigid search: FFTShape complementarity, desolvation energy, and electrostatics.

Energy minimization and re-scoringFree for academics

Point to note:

The proper treatment of flexibility in protein–protein docking is still an active field of research. You first should analyzed your proteins in order to define their conformational space and then choose the most suitable method for your docking problem.

(ABT/DIC/01/2014 (No. AAU/ABT/DIT/Advt. 01/2015/111 Dtd. 19-05-2015)

Walk in interview for the following position will be held on 6th June, 2015 at 10.00AM in the Office Chamber of the undersigned. Candidates may appear for the interview with bio-data, reprints / publication / thesis etc and passport size photographs, original and attested copies of all testimonials etc, which must be presented at the time of interview. The applicants may submit their resume in advance tomkmodi@aau.ac.in.

Research Associate

Ph.D. in Biotechnology/ Bioinformatics. Or

Masters degree in Biotechnology/Bioinformatics with minimum 3(three) years research experience

Desirable : Experience in Bioinformatics as evidenced from published research

Rs 36,000+HRA for the 1st two years and 38,000+HRA for the 3rd year.

Senior Research Fellow

Master Degree in Biotechnology/ Bioinformatics. With 2 (two) years Experience in Bioinformatics as evidenced from Course work/ Diploma/Published research

Rs 28,000+HRA for NET qualified candidate/Professional degree holder

Rs 18,000+HRA for non-NET qualified general degree holder

Junior Research Fellow

Master Degree in Biotechnology/ Bioinformatics/Computer Science/Computer Application

Desirable: Experience in Bioinformatics as evident from Course work/ Diploma/Published research

Rs 25,000+HRA for NET qualified candidate/Professional degree holder

Rs 16,000+HRA for non-NET qualified general degree holder

Note: Term and conditions will be as per the DBT, Govt of India guidelines.

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Download 

http://arthropods.eugenes.org/EvidentialGene/trassembly.html

https://sourceforge.net/p/evidentialgene/blog/

Address of the bookmark: http://arthropods.eugenes.org/EvidentialGene/trassembly.html

Applications are invited for the post of Senior Research Fellow- SRF (1) and Junior Research Fellow- JRF (1) to be appointed in a SERB-funded major research project entitled “Biochemical and functional properties of Synechocystis Glutathione S-transferase(s)” sanctioned to Dr. Timir Tripathi, Molecular and Structural Biophysics Laboratory, Department of Biochemistry, NEHU, Shillong.

Essential Qualifications: For both positions M.Sc. or equivalent with a good academic record is a prerequisite.

For Project-SRF, experience in bioinformatics/computational biology is required, which should be evident by atleast one good publication.

For JRF position, freshers can also apply.

Stipend: As per SERB norms.

Interested students can email their detailed bio-data including mobile number and recent photograph to msb.biochem@gmail.com, latest by 20.06.15. The hard copy is not required. The date of interview will be informed after primary scrutiny of the applications. No TA/DA will be paid if called for interview. For details of the research work of the PI’s group kindly visit www.ttripathi.webs.com

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gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

#Find the reverse complement of a DNA string.
#Given: A DNA string Pattern.
#Return: Pattern, the reverse complement of Pattern.

use strict;
use warnings;

my $string="AAAACCCGGT";
my $finalString="";
my %hash = (
    "C" => "G",
    "A" => "T",
    "T" => "A",
    "G" => "C",
);

for (my $aa=0; $aa<=(length($string)-1); $aa++) {
    my $char=substr $string, $aa, 1;
    #print $hash{$char};
    $finalString="$hash{$char}"."$finalString";
}

print $finalString;
print "\n";

ashr - https://github.com/stephens999/ashr, https://cran.r-project.org/web/packages/ashr/index.html

consensusDE - https://bioconductor.org/packages/release/bioc/html/consensusDE.html

DESeq2 - https://bioconductor.org/packages/release/bioc/html/DESeq2.html

edgeR - https://bioconductor.org/packages/release/bioc/html/edgeR.html

limma - https://kasperdanielhansen.github.io/genbioconductor/html/limma.html  https://bioconductor.org/packages/release/bioc/html/limma.html

MetaCycle - https://cran.r-project.org/web/packages/MetaCycle/index.html, https://github.com/gangwug/MetaCycle

RUVSeq - https://bioconductor.org/packages/release/bioc/html/RUVSeq.html

SARTools - https://github.com/PF2-pasteur-fr/SARTools

tximport - https://github.com/mikelove/tximport

Monthly fellowship (in rupee): 5,000/-

Traineeship

First Class M.Sc Bioinformatics/ Biotechnology/ Botany

Studentship: 5,000/-

M.Phil/M.Tech Bioinformatics/ Biotechnology/ any branch of Life Science students for doing their thesis work in the area of Bioinformatics.

Age limit as on 1.1.2015, 28 years. Age relaxation will be provided for SC, ST, OBC candidates as per Govt. norms.

Interested candidates may appear for walk-in-interview on 16th June 2015 at 10.30 am at JNTBGRI, Palode, Thiruvananthapuram. The candidate should report to the Office at Palode before 10.00 am

More at http://www.jntbgri.in/jntbgri/news/File0001.pdf

Following are the comprehensive list of visualization tools for biological pathways:

BiNA

Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures

http://bina.unipax.info/

BioTapestry

Interactive tool for building, visualizing and sharing gene regulatory network models over the web

http://www.biotapestry.org/

Caleydo

Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets

http://www.caleydo.org/

CellDesigner

A modeling tool for biochemical networks

http://www.celldesigner.org/

Edinburgh Pathway Editor

Edit and draw pathway diagrams

http://epe.sourceforge.net/SourceForge/EPE.html

GenMAPP

Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes

http://www.genmapp.org/

Ingenuity IPA

Data integration platform and manually annotated pathways

http://tinyurl.com/IngenuityPath

JDesigner

Graphical modeling environment for biochemical reaction networks

http://jdesigner.sourceforge.net/Site/JDesigner.html

KaPPA View

Plant pathways

http://kpv.kazusa.or.jp/

KEGG Atlas

Interactive Kyoto Encyclopedia of Genes and Genomes pathways

http://www.genome.jp/kegg/

Omix 

Visualizing multi-omics data in metabolic networks

https://www.omix-visualization.com

PathVisio 

Biological pathway analysis software that allows drawing, editing and analysis of biological pathways

http://www.pathvisio.org/

VitaPad 

Application to visualize biological pathways and map experimental data to them

http://tinyurl.com/vitapad/

Web tools for pathways

ArrayXPath 

Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG

http://tinyurl.com/ArrayXPath/

GEPAT 

Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts

http://gepat.sourceforge.net/

iPath 

Web-based tool for the visualization, analysis and customization of pathway maps

http://pathways.embl.de/

Kegg-Based Viewer 

KEGG-based pathway visualization tool for complex high-throughput data

http://www.g-language.org/data/marray/

MapMan 

User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes

http://mapman.gabipd.org/web/guest/mapman

MetPA 

Analysis and visualization of metabolomic data within the biological context of metabolic pathways

http://metpa.metabolomics.ca

Omics Viewer 

Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)

http://www.biocyc.org/

Pathway Explorer

Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them

http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml

Pathway projector 

Zoomable pathway browser using KEGG atlas and Google Maps API

http://www.g-language.org/PathwayProjector/

PATIKA 

Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework

http://www.cs.bilkent.edu.tr/~patikaweb/

Reactome SkyPainter 

Visualization of over-represented pathways and reactions from gene lists

http://www.reactome.org/skypainter-2

WikiPathways

Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community

http://www.wikipathways.org/