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/

Name of the College: Karpagam University, Coimbatore

Date of official publication: 15th April 2015

The newspaper wherein this job advertised: The Hindu Newspaper

Name of the posts: Senior Professors, Professors, Associate Professors and Assistant Professors

Departments:
Bioinformatics
Biotechnology
Qualifications/Eligibility: The candidates should have qualifications as M.E/M.Tech/M.A/M.Com/MBA/M.Sc/M.Phil/NET/SLET/Ph.D

Job Location: Coimbatore, TN

Salary: As per college norms

How to apply: Interested and eligible candidates are requested to apply online at http://www.karpagamuniversity.edu.in/career

Last date: As soon as possible from 15th April 2015

Reference: The Hindu Newspaper dated 15-04-2015, Coimbatore edition on 14th page

Perform secondary structure predictions on protein sequences.

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/

Upgrading to R 3.2.0 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) #load / install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.).

If you are an R blogger yourself you are invited to add your own R content feed to this site (Non-English R bloggers should add themselves- here)

NEW FEATURES

• anyNA() gains a recursive argument.
• When x is missing and names is not false (including the default value), Sys.getenv(x, names) returns an object of class "Dlist" and hence prints tidily.
• (Windows.) shell() no longer consults the environment variable SHELL: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). R_SHELL, the preferred way to select a non-default shell, can be used instead.
• Some unusual arguments to embedFonts() can now be specified as character vectors, and the defaults have been changed accordingly.
• Functions in the Summary group duplicate less. (PR#15798)
• (Unix-alikes.) system(cmd, input = ) now uses ‘shell-execution-environment’ redirection, which will be more natural if cmd is not a single command (but requires a POSIX-compliant shell). (Wish of PR#15508)
• read.fwf() and read.DIF() gain a fileEncoding argument, for convenience.
• Graphics devices can add attributes to their description in .Device and .Devices. Several of those included with R use a "filepath" attribute.
• pmatch() uses hashing in more cases and so is faster at the expense of using more memory. (PR#15697)
• pairs() gains new arguments to select sets of variables to be plotted against each other.
• file.info(, extra_cols = FALSE) allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists.
• New function dir.exists() in package base to test efficiently whether one or more paths exist and are directories.
• dput() and friends gain new controls hexNumeric and digits17 which output double and complex quantities as, respectively, binary fractions (exactly, see sprintf("%a")) and as decimals with up to 17 significant digits.
• save(), saveRDS() and serialize() now support ascii = NA which writes ASCII files using sprintf("%a") for double/complex quantities. This is read-compatible with ascii = TRUE but avoids binary->decimal->binary conversions with potential loss of precision. Unfortunately the Windows C runtime’s lack of C99 compliance means that the format cannot be read correctly there in R before 3.1.2.
• The default for formatC(decimal.mark =) has been changed to be getOption("OutDec"); this makes it more consistent with format() and suitable for use in print methods, e.g. those for classes "density", "ecdf", "stepfun" and "summary.lm".

  getOption("OutDec") is now consulted by the print method for class "kmeans", by cut(), dendrogram(), plot.ts() and quantile() when constructing labels and for the report fromlegend(trace = TRUE).

  (In part, wish of PR#15819.)

• printNum() and hence format() and formatC() give a warning if big.mark and decimal.mark are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed).
• merge() can create a result which uses long vectors on 64-bit platforms.
• dget() gains a new argument keep.source which defaults to FALSE for speed (dput() and dget() are most often used for data objects where this can make dget() many times faster).
• Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.
• A number of macros have been added in the new ‘share/Rd’ directory for use in package overview help pages, and promptPackage() now makes use of them.
• tools::parse_Rd() gains a new permissive argument which converts unrecognized macros into text. This is used by utils:::format.bibentry to allow LaTeX markup to be ignored.
• options(OutDec =) can now specify a multi-byte character, e.g., options(OutDec = "u00b7") in a UTF-8 locale.
• is.recursive(x) is no longer true when x is an external pointer, a weak reference or byte code; the first enables all.equal(x, x) when x .
• ls() (aka objects()) and as.list.environment() gain a new argument sorted.
• The "source" attribute (which has not been added to functions by R since before R version 2.14.0) is no longer treated as special.
• Function returnValue() has been added to give on.exit() code access to a function’s return value for debugging purposes.
• crossprod(x, y) allows more matrix coercions when x or y are vectors, now equalling t(x) %*% y in these cases (also reported by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in more cases with vector arguments.
• Utility function dynGet() useful for detecting cycles, aka infinite recursions.
• The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.
• apply(m, 2, identity) is now the same as the matrix m when it has named row names.
• A new function debuggingState() has been added, allowing to temporarily turn off debugging.
• example() gets a new optional argument run.donttest and tools::Rd2ex() a corresponding commentDonttest, with a default such that example(..) in help examples will run donttest code only if used interactively (a change in behaviour).
• rbind.data.frame() gains an optional argument make.row.names, for potential speedup.
• New function extSoftVersion() to report on the versions of third-party software in use in this session. Currently reports versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and the iconv implementation.

  A similar function grSoftVersion() in package grDevices reports on third-party graphics software.

  Function tcltk::tclVersion() reports the Tcl/Tk version.

• Calling callGeneric() without arguments now works with primitive generics to some extent.
• vapply(x, FUN, FUN.VALUE) is more efficient notably for large length(FUN.VALUE); as extension of PR#16061.
• as.table() now allows tables with one or more dimensions of length 0 (such as as.table(integer())).
• names(x) now clears the names of call and ... objects.
• library() will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path.
• A new plot() method for class "raster" has been added.
• New check_packages_in_dir_changes() function in package tools for conveniently analyzing how changing sources impacts the check results of their reverse dependencies.
• Speed-up from Peter Haverty for ls() and methods:::.requirePackage() speeding up package loading. (PR#16133)
• New get0() function, combining exists() and get() in one call, for efficiency.
• match.call() gains an envir argument for specifying the environment from which to retrieve the ... in the call, if any; this environment was wrong (or at least undesirable) when thedefinition argument was a function.
• topenv() has been made .Internal() for speedup, based on Peter Haverty’s proposal in PR#16140.
• getOption() no longer calls options() in the main case.
• Optional use of libcurl (version 7.28.0 from Oct 2012 or later) for Internet access:
  • capabilities("libcurl") reports if this is available.
  • libcurlVersion() reports the version in use, and other details of the "libcurl" build including which URL schemes it supports.
  • curlGetHeaders() retrieves the headers for http://, https://, ftp:// and ftps:// URLs: analysis of these headers can provide insights into the ‘existence’ of a URL (it might for example be permanently redirected) and is so used in R CMD check --as-cran.
  • download.file() has a new optional method "libcurl" which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.
  • url() has a new method "libcurl" which handles more URL schemes and follows redirections. The default method is controlled by a new option url.method, which applies also to the opening of URLs via file() (which happens implicitly in functions such as read.table.)
  • When file() or url() is invoked with a https:// or ftps:// URL which the current method cannot handle, it switches to a suitable method if one is available.
• (Windows.) The DLLs ‘internet.dll’ and ‘internet2.dll’ have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an Rsession.

  The Windows internet functions are still selected by flag –internet2 or setInternet2(). This can be overridden for an url() connection via its new method argument.

  download.file() has new method "wininet", selected as the default by –internet2 or setInternet2().

• parent.env<- can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar.
• New function isLoadedNamespace() for readability and speed.
• names(env) now returns all the object names of an environment env, equivalently to ls(env, all.names = TRUE, sorted = FALSE) and also to the names of the corresponding list,names(as.list(env, all.names = TRUE)). Note that although names() returns a character vector, the names have no particular ordering.
• The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.
• New function trimws() for removing leading/trailing whitespace.
• cbind() and rbind() now consider S4 inheritance during S3 dispatch and also obey deparse.level.
• cbind() and rbind() will delegate recursively to methods::cbind2 (methods::rbind2) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity).
• (Windows.) download.file(quiet = FALSE) now uses text rather than Windows progress bars in non-interactive use.
• New function hsearch_db() in package utils for building and retrieving the help search database used by help.search(), along with functions for inspecting the concepts and keywords in the help search database.
• New function .getNamespaceInfo(), a no-check version of getNamespaceInfo() mostly for internal speedups.
• The help search system now takes keyword entries in Rd files which are not standard keywords (as given in ‘KEYWORDS’ in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.
• New lengths() function for getting the lengths of all elements in a list.
• New function toTitleCase() in package tools, tailored to package titles.
• The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elements. (For cbind(), wish of PR#16198.)
• The default method of image() has an explicit check for a numeric or logical matrix (which was always required).
• URLencode() will not by default encode further URLs which appear to be already encoded.
• BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima() fitted models, as nobs(mod) now gives the number of “used” observations for such models. This fixes PR#16198, quite differently than proposed there.
• The print() methods for "htest", "pairwise.htest" and "power.htest" objects now have a digits argument defaulting to (a function of) getOption("digits"), and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases.
• Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.
• The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.
• unzip() will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to PR#16243).
• methods() reports S4 in addition to S3 methods; output is simplified when the class argument is used. .S3methods() and methods::.S4methods() report S3 and S4 methods separately.
• Higher order functions such as the apply functions and Reduce() now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves PR#16093.

More at http://cran.rstudio.com/

Reference: http://www.r-bloggers.com/r-3-2-0-is-released-using-the-installr-package-to-upgrade-in-windows-os/

SRF/ JRF job vacancies in National Institute of High Security Animal Diseases (ICAR)

Name of Post : JRF

No. of Post : 01

Qualification : M.V.Sc or M.Tech./M.Sc. (preferably with NET qualification) in one of following disciplines. (Biotechnology/Molecular Biology/Genetics/Microbiology/Bioinformatics or equivalent Life Sciences discipline). Desirable: Working Knowledge in the areas of Recombinant DNA Techniques, Cell Culture, Handling Laboratory Animals, Genomics.

Emolument : Rs.16,000/-

Age Limit : Up to 30 years

Name of Post : Project Assistant

No of Post : 01

Qualifications : First class M.Sc. /B.E/B.Tech. in one of the following disciplines Biotechnology/ Bioinformatics/ Microbiology or equivalent Life Sciences discipline). Desirable : Exposure of working in research environment, Good command over written/spoken English and computer applications.

Emolument : Rs.8000/-

Age Limit : Upto 28 years

Name of Post : Project Assistant

No of Post : 01

Qualification : First class M.Sc. /B.V.Sc. and A.H., B.Tech. /B.E. in Life Sciences and related areas. Desirable: Exposure of working in research environment, Good command over written/type written/spoken English and computer applications.

Emoluments : Rs. 8000/-

Age Limit : Up to 28 years
How to apply

Desirous candidates may send their applications by e-mail (techcell@hsadl.nic.in ) followed by post in the prescribed proforma latest by 11/05/2015. Walk-in-Interview will be held at NIHSAD, Kokta Road, Anand Nagar, Bhopal-462022.

http://www.nihsad.nic.in/pdf/Advt.pdf

Location : Kulu

Job Category : Govt Jobs, Research

Last Date : 20 May 2015

Job Type : Full Time

Hiring Process : Walk - In
IIT Mandi - Job Details
IIT Mandi

Project Associate Bioinformatics Job vacancies in IIT Mandi on purely temporary

Project: “Exploring the Human Microbiome: A hunt for the candidates for Pre- and Pro-biotics.”

Minimum Qualification and Experience: M.Sc. in Bioinformatics OR B.Tech / BE in Bioinformatics OR M. Sc. in Biotechnology / Life sciences or related areas with Diploma or relevant experience in Bioinformatics OR B.Tech in Biotechnology / Computer Science or MCA or B. Sc. in Life Sciences or related areas with PG diploma in Bioinformatics. Candidates with experience in NGS data handling and analysis will be preferred. Tenure: Initially for one year, extendable based upon performance.

No of Posts: 01

Salary: Rs. 12000- 18000/- per month.

How to apply

Interested candidates can come for a Walk-in-Interview on 20th May 2015 starting at 8:30 AM at the Academic Block, Indian Institute of Technology (IIT), Mandi, Vallabh College Campus, Near Bus Stand, Mandi, HP. The candidates should bring along their curriculum vitae (CV) and copies of educational and experience certificates. In case of any queries please contact: Dr. Tulika Prakash Srivastava (Principal Investigator), Indian Institute of Technology Mandi, Near Bus Stand Mandi - 175 001, Himachal Pradesh.

More at

http://www.iitmandi.ac.in/administration/advrt/Walk-in-interview_Ad.pdf

Project Assistant (Level-II) job position in Central Food Technological Research Institute (CFTRI) on a temporary contractual basis in the research project (GAP 0469) funded by Science & Engineering Research Board (SERB), Government of India, New Delhi tenable at the Lipidomics Centre, CSIR-CFTRI, Mysore, Karnataka

Name of the Position :

Qualification : First class M. Sc. in Biochemistry/Microbiology/Genetics/ Bioinformatics with good academic record and preferably with experience in molecular biology techniques and basic knowledge of molecular biology and biological chemistry

Emoluments : Rs. 12,000/- per month (Consolidated)

Age Limit : The upper age limit for applying shall be 28 years (as on 22-5-2015), which is relaxed for candidates belonging to Scheduled Castes/Schedule Tribes, Women, Persons with Disabilities (PWD) and OBCs as per GoI norms.

How to apply

Eligible candidates may send their complete Bio-data with e-mail address/contact phone number along with attested copies of the necessary certificates through post to Prof. Ram Rajasekharan, Lipidomics Centre, Department of Lipid Science, CSIR-CFTRI, Mysore-570 020, Karnataka (email: ram@cftri.res.in) on or before 22.05.2015

More at http://www.cftri.com/pa_gap0469.html

Details will be available at: http://nrcorchids.nic.in/Employments/Vacancy%20-%20JRF.pdf