Following are the list of standalone applications for network analysis:

Arena 3D

3D visualization of multi-layer networks

http://www.arena3d.org

Biana

Data integration and network management

http://sbi.imim.es/web/BIANA.php

BioLayout Express 3D 

2D/3D network visualization

http://www.biolayout.org/

BiologicalNetworks 

Efficient integrated multi-level analysis of microarray, sequence, regulatory and other data

http://www.biologicalnetworks.org

BioMiner

Modeling, analyzing and visualizing biochemical pathways and networks

http://www.zbi.uni-saarland.de/chair/projects/BioMiner

Cell Illustrator 

Petri nets for modeling and simulating biological networks

http://www.cellillustrator.com

COPASI

Analysis of biochemical networks and their dynamics

http://www.copasi.org/

Cytoscape 

Network visualization and analysis. Over 200 plugins [60]

http://www.cytoscape.org/

Dizzy

Chemical kinetics stochastic simulation software

http://magnet.systemsbiology.net/software/Dizzy/

DyCoNet

Gephi plugin that can be used to identify dynamic communities in networks

https://github.com/juliemkauffman/DyCoNet

GENeVis 

Network and pathway visualization

http://tinyurl.com/genevis/

GEPHI 

Interactive visualization and exploration for any network and complex system, dynamic and hierarchical graph.

https://gephi.org

Igraph

Collection of network analysis tools with the emphasis on efficiency, portability and ease of use

http://igraph.sourceforge.net

Medusa

Semantic and multi-edged simple networks

https://sites.google.com/site/medusa3visualization/

NAViGaTOR

Visualizing and analyzing protein-protein interaction networks

http://tinyurl.com/navigator1/

N-Browse

Interactive graphical browser for biological networks

http://www.gnetbrowse.org/

NeAT

Topological and clustering analysis of networks

http://rsat.ulb.ac.be/neat/

Ondex 

Data integration and visualization of large networks

http://www.ondex.org/

Osprey

Visualization and annotation of biological networks

http://biodata.mshri.on.ca/osprey/servlet/Index

Pajek 

Analysis and visualization of large networks and social network analysis

http://vlado.fmf.uni-lj.si/pub/networks/pajek/

PathwayAssist 

Navigation and analysis of biological pathways, gene regulation networks and protein interaction maps.

http://www.ariadnegenomics.com/downloads/

PIVOT 

Layout algorithms for visualizing protein interactions and families

http://acgt.cs.tau.ac.il/pivot/

ProCope 

Prediction and evaluation of protein complexes from purification data experiments

http://www.bio.ifi.lmu.de/Complexes/ProCope/

ProViz 

Visualization and exploration of interaction networks. Gene Ontology and PSI-MI formats supported

http://cbi.labri.fr/eng/proviz.htm

SpectralNET 

Network analysis and visualizations. Scatter plots and dimensionality reduction algorithms

https://www.broadinstitute.org/software/spectralnet

Tulip 

Enables the development of algorithms, visual encodings, interaction techniques, data models and domain-specific visualizations

http://tulip.labri.fr/TulipDrupal/

VANESA 

Automatic reconstruction and analysis of biological networks and Petri nets based on life-science database information

http://agbi.techfak.uni-bielefeld.de/vanesa/

VANTED 

Network reconstruction, data visualization, integration of various data types, network simulation

http://tinyurl.com/vanted/

yEd

Creation of diagrams manually and import external data

http://tinyurl.com/yEdGraph/

Web tools for network analysis

APID 

Unified protein-protein interactions from BIND, BioGRID, DIP, HPRD, IntAct and MINT

http://bioinfow.dep.usal.es/apid/

Arcadia 

Translates text-based descriptions of biological networks (SBML files) into standardized diagrams (Systems Biology Graphical Notation Process Description maps)

http://arcadiapathways.sourceforge.net/

AVIS 

Viewer for signaling networks

http://actin.pharm.mssm.edu/AVIS2

bioPIXIE 

Discovery of biological networks from diverse functional genomic data

http://pixie.princeton.edu/pixie

CellPublisher

Interactive representations of biochemical processes

http://cellpublisher.gobics.de/

Graphle

Distributed network exploration and visualization of interactive large, dense graphs

http://tinyurl.com/graphle/

GraphWeb 

Web server for graph-based analysis of biological networks

http://biit.cs.ut.ee/graphweb/

Hubba

Web-based service to explore the essential nodes in a network

http://hub.iis.sinica.edu.tw/Hubba

NetworkBLAST 

Analysis of protein interaction networks across species to infer protein complexes that are conserved in evolution

http://www.cs.tau.ac.il/~bnet/networkblast.htm

Pathview 

Tool set for pathway-based data integration and visualization

http://Pathview.r-forge.r-project.org/

PINA 

Integrated platform for protein interaction network construction, filtering, analysis, visualization and management

http://cbg.garvan.unsw.edu.au/pina/home.do

ReMatch 

Web-based tool for integration of user-given stoichiometric metabolic models into a database collected from public data sources

http://www.cs.helsinki.fi/group/sysfys/software/rematch/

SNOW 

Gene mapping on a reference or human protein-protein interaction network that SNOW hosts

http://snow.bioinfo.cipf.es

STITCH 

Resource to explore known and predicted interactions of chemicals and proteins

http://stitch.embl.de/

STRING

Protein interaction networks and integration of data such as genomic context, high-throughput experiments, conserved coexpression and previous knowledge derived from the literature

http://string-db.org

TVNViewer 

An interactive visualization tool for exploring networks that change over time or space

http://www.sailing.cs.cmu.edu/main/?page_id=545

tYNA 

System for managing, comparing and mining multiple networks

http://tyna.gersteinlab.org/tyna/

VisANT 

Visualization, mining, analysis and modeling of biological networks, metabolic networks and ecosystems

http://visant.bu.edu/

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

Other tools

https://github.com/shenwei356/taxonkit

• ETE, version: 3.1.1
• BioPython, version: 1.73
• taxadb, version: 0.10.1
• TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

Name of the post: Senior Research Fellow (SRF)
Duration: 2 year
Salary: Rs. 28000/- per month + 30% HRA
Eligibility: MSc (life sciences) with 2 years research experience, NET/GATE qualified
Desirable: Experience in the field of Genomics, Epigenomics & Bioinformatics
SELECTION PROCEDURE FOR ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI) – SENIOR RESEARCH FELLOW POST:

Candidates can apply on or before 15/03/2015
No Detailed information about the selection process is mentioned in the recruitment notification
HOW TO APPLY FOR SENIOR RESEARCH FELLOW VACANCY IN ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI):

Deadline: 15.03.15 Submit your C.V in Room No. 2099 (Molecular Cytogenetics Lab), 2nd floor, Reproductive Biology, All India Institute of Medical Sciences, New Delhi-110029 or Email CV to: ashutoshhalder@gmail.com Your CV should include the details of your work experience & degrees along with two references with e-mail and contact number Only 10 shortlisted (on merit) candidates will be invited for interview. No TA/DA will be applicable for the same

Central University of Jharkhand has been granted funds by the Department of Biotechnology (DBT), Govt. of India to establish “DBT-Boost to CUJ Interdisciplinary Life Sciences Departments for Education and Research” Applications are invited for the Assistant Professor on purely temporary basis. The appointments shall be initially for a period of one year, renewable every year depending on the satisfactory performance, till the end of project.

Position: ASSISTANT PROFESSOR (Total 03)
Salary: 45,000/- (fixed) per month
Essential Qualifications: i. Good academic record with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the master’s degree level with specialization in Biodiversity and Systematic/ Systems Biology/ Biophysics/ Bioinformatics from an Indian University, or an equivalent degree from an accredited foreign university. ii. Besides fulfilling the above qualifications, the candidates must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/SET. iii. Notwithstanding anything contained in i. and ii. candidates, who are or have been awarded Ph.D Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulation, 2009, shall be exempted from therequirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor. iv. NET/SLET/SET shall also not be required for such disciplines for which NET/SLET/SET in not conducted.
Desirable: Preference will be given to candidates having Ph.D in any of the above mentioned areas with NET

IMPORTANT DATES TO REMEMBER :

Last Date to Apply for this job 24/3/2015

REFERENCE:

Central University of Jharkhand (CUJ) Recruitment 2015 – Advt. No.: CUJ/Advt./14-15/15 Date: 26th Feb. 2015.

More at http://cuj.ac.in/careers.php

http://molbiolabccsumrt.webs.com/

Applications are invited for one post of RA in a DBT funded research project “Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) Scheme of BTISet”.

Candidate should have a Ph.D. degree in Bioinformatics/Biotechnology/Genetics and Plant Breeding with adequate experience in the area of Bioinformatics. If a suitable candidate for the post of RA is not available, a JRF/SRF may be appointed.

Candidate for the post of JRF/SRF should have Master’s degree in relevant subject with adequate experience in the area of Bioinformatics and should be NET/DBT-BINC qualified

Interested candidates may send their bio-data to Prof. H. S. Balyan (hsbalyan@gmail.com) (in exceptional case, bio-data may also be submitted at the time of interview) and attend the interview on Monday, March 30, 2015 at 11:00 AM in the Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut. Candidates shall bring their original documents at the time of interview for verification. No interview letters will be issued and no TA/DA will be paid.

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Address of the bookmark: http://www.tutorialspoint.com/codingground.htm