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WSCC – 2013

Radha Agarkar — Sat, 09 Nov 2013 18:35:18 -0600

DST-SERB Winter School on Computational Chemistry (WSCC – 2013)

December 9-13, 2013

Organized By Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar – 388120, Gujarat

Topics to be covered

The topics and lectures including practical sessions planned are summarized as follows:

Topics of Teaching and Research

1. Review of postulates of quantum mechanics; Some key concepts from linear algebra; The Schrodinger equation; Particle in one dimensional box; Hydrogenic orbitals; The helium atom; many electron; Problem solving. -

[Prof. R. B. Sunoj, IITB, Mumbai]

2. The Born–Oppenheimer Approximations; Qualitative MO Theory; Potential energy surfaces; Variational Theorem, Perturbation theory; Problem solving.

[Dr. Narahari Sastry, CSIR-IICT, Hyderabad]

3. Hartree Products; Slater determinants; Antisymmetry principle; The Hartree-Fock approximation; Restricted and Unrestricted Hartree–Fock; Koopmans’ theorem; Electron correlation; Electron density; Examples and problems.

[Prof. S. R. Gadre, IITK, Kanpur]

4. Hückel Theory, Bond order and charge density analysis; Extended Hückel Theory; Semi-Empirical Methods: e.g. CNDO; AM1; PM3; Parameterization; Advantages and Limitations of Semi-Empirical Methods. Applications.

[Prof. S. P. Gejji, Univ. Pune]

5. ab initio methods; Classification of Basis Sets; Conﬁguration Interaction; Møller–Plesset perturbation theory; Coupled Cluster theory; Solvation Models; Continuum Solvation Models.

[Dr. C. H. Suresh, CSIR- NIIST, Thiruvananthapurum]

6. Density Functional Theory: The Hohenberg-Kohn theorems; The Kohn-Sham equations; Local density and generalized gradient approximations; The LCAO Ansatz in the KS equations; Applications of DFT.

[Prof. M. S. Gopinathan, IISER, Thiruvananthapurum]

7. Hybrid or hyper-GGA methods; beyond static DFT; Beyond LDA and GGA; Self-interaction correction; Dispersion corrected functional; Time-dependent DFT (TD-DFT): Runge-Gross theorem; Conceptual DFT: Fukui function; Global hardness and softness; Local hardness and softness; Electronegativity and the Electronic Chemical Potential.

[Dr. D. K. Maity, BARC, Mumbai]

8. Molecular Mechanics

Introduction; Empirical Force Fields; Force Field Parameterization; Differences in Force Fields; Energy Minimization; Limitations of Molecular Mechanics Models.

[Dr. Sudhir Kulkarni, Vlife Technologies, Pune ]

9. Statistics and QSAR

Introduction; Elementary Statistical Measures; Correlation between Two Sets of Data; Correlation between Many Sets of Data; Quantitative Structure–Activity Relationships (QSAR); Structure property correlation; Molecular descriptors; Application in biological systems; 3D-QSAR

[Dr. Sudhir Kulkarni, Vlife Technologies, Pune ]

10. Qualitative Valence Bond Theory:

Roots of VB theory; The two-electron bond; Polyatomic molecules; hybridization; Writing and representing VB wave functions; Bridges between Molecular Orbital (MO) and VB theories; Applications.

[Prof. S. Ramashesha, IISc, Bangalore]

11. Molecular dynamics

Equations of Motion; Dynamics Trajectories: Integrating Newton's Laws; Ensembles; Periodic boundary conditions; Monte Carlo Methods; Classical and ab initio molecular dynamics; Applications.

[Dr. Nisanth Nair, IITK, Kanpur]

More Info : https://sites.google.com/site/dstserbwscc2013

Make Genomic Research Less Ethnically-Biased

Shikha Logwani — Wed, 30 Oct 2013 16:08:17 -0500

Mexican billionaire Carlos Slim Hélu, the world’s 2nd-richest man, is giving an additional $74 million to a genomics center in Boston in order to right a bias in the field–a kind of scientific racism, you might call it. The problem: most samples of DNA analyzed in biomedical research come from people of European descent.

Find more detail news at http://www.forbes.com/sites/erincarlyle/2013/10/30/carlos-slim-gives-another-74-million-to-make-genomic-research-less-ethnically-biased/?utm_campaign=forbesfbsf&utm_source=facebook&utm_medium=social

BEReX : Biomedical Entity-Relation eXplorer

Rahul Nayak — Wed, 30 Oct 2013 15:53:26 -0500

BEReX is a new biomedical knowledge integration, search, and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PharmGKB, BioGRID, GO, HPRD, and MSigDB) and delineates an integrated network by combining the information available from these databases. Users search the integrated network by entering keywords and BEReX returns a sub-network matching the keywords. The resulting graph can be explored interactively. BEReX allows users to find the shortest paths between two remote nodes; find the most relevant drugs, diseases, pathways and so on, related to the current network; expand the network by particular types of entities and relations; and modify the network by removing or adding selected nodes. BEReX is implemented as a stand-alone Java application.

More at http://infos.korea.ac.kr/berex

News reference @ http://infos.korea.ac.kr

An entire genome written in lab

Rahul Nayak — Fri, 25 Oct 2013 09:43:03 -0500

This is the first time ever the genetic code has been fundamentally changed. The breakthrough is a huge step forward in synthetic biology and opens up the possibility of turning re-coded bacteria into biofactories, capable of producing potent new forms of protein that could fight disease or generate sustainable materials.

More @ http://news.yale.edu/2013/10/17/researchers-rewrite-entire-genome-and-add-healthy-twist

News Reference: Yale news

Image Source: Sciencedaily.

RNA-Seq Data Pathway and Gene-set Analysis Workflows

Jit — Fri, 25 Oct 2013 08:00:48 -0500

It describe the GAGE (Luo et al., 2009) /Pahview (Luo and Brouwer, 2013) workflows on RNA-Seq data pathway analysis and gene-set analysis. The gage package (2.12.0) now includes a new tutorial, “RNA-Seq Data Pathway and Gene-set Analysis Workflows“.

First cover a full workflow from preparation, reads counting, data preprocessing, gene set test, to pathway visualization in about 40 lines of codes. The same workflow can be used for GO analysis or other types of gene set analysis too. We also describe joint workflows, i.e. to do gene-level analysis using one of the major RNA-Seq analysis tools, DEseq/DEseq2, edgeR, limma and Cufflinks, and feed the results into GAGE/Pahview for pathway analysis or visualization. All these workflows are implemented in R/Bioconductor.

The work ows cover the most common situations and issues for RNA-Seq data pathway analysis. Issues like data quality assessment are relevant for data analysis in general yet out the scope of this tutorial. Although we focus on RNA-Seq data here, but pathway analysis work ow remains similar for microarray, particularly step 3-4 would be the same. Please check gage and pathview vigenttes for details.

Note: You need to update to current release versions of R(3.0.2)/ Bioconductor(2.13) to use all the features.

Reference:

Please check it out:
http://bioconductor.org/packages/release/bioc/html/gage.html
http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

PubMed opens for comment

Rahul Nayak — Thu, 24 Oct 2013 12:40:17 -0500

The informal conversations that researchers have at scientific meetings look set to move online, if a new initiative by the US National Center for Biotechnology Information (NCBI) has its way. On 22 October, the NCBI of Bethesda, Maryland, launched the pilot phase of a programme called PubMed Commons. This will allow users to comment on published abstracts on the PubMed website, which indexes some 22 million papers.

For now, only a select group of researchers and their invited guests can use the system. But the NCBI's director David Lipman, who helped to develop the programme, says that soon any PubMed author will be allowed to comment under his or her real name and anyone will be able to read the comments.

More @ http://www.nature.com/news/pubmed-opens-for-comment-1.14023

News source Nature.

The anatomy of successful computational biology software

Jitendra Narayan — Thu, 10 Oct 2013 11:53:08 -0500

Creators of software widely used in computational biology discuss the factors that contributed to their success

Nature Biotechnology spoke with Altschul and several other originators of computational biology software programs widely used today (Table 1). The conversations explored what makes certain software tools successful, the unique challenges of developing them for biological research and how the field of computational biology, as a whole, can move research agendas forward. What follows is an edited compilation of interviews.

Detail @ http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html

News Source @ Nature

Biggest Human Brain Project (HBP) launched!!!

Rahul Agarwal — Mon, 07 Oct 2013 19:50:55 -0500

"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledge, and prioritising future experiments.

In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new treatments, drastically lowering the cost of drug discovery.

In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence."

Source: http://www.forbes.com/sites/jenniferhicks/2013/10/07/the-human-brain-project-begins/

(https://www.facebook.com/humanbrainproj/info)

Home Page:

https://www.humanbrainproject.eu/

Jobs:

https://www.humanbrainproject.eu/participate/jobs

Programming language to build synthetic DNA

Jit — Mon, 30 Sep 2013 16:37:24 -0500

A team led by Georg Seelig (http://homes.cs.washington.edu/~seelig/index.html) at University of Washington has developed a programming language for chemistry that it hopes will streamline efforts to design a network that can guide the behavior of chemical-reaction mixtures in the same way that embedded electronic controllers guide cars, robots and other devices. In medicine, such networks could serve as “smart” drug deliverers or disease detectors at the cellular level.

Reference & More @

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html

http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/

Image source: washington.edu

Petrol from Ecoli

Rahul Agarwal — Mon, 30 Sep 2013 10:31:17 -0500

"In recently published paper (entitled "Microbial Production of Short-chain Alkanes") in Nature journal on September 29, a group of genius Korean researchers led by Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST) reported, for the first time, the development of a novel strategy for microbial gasoline production through metabolic engineering of E. coli.

The research team engineered the fatty acid metabolism to provide the fatty acid derivatives that are shorter than normal intracellular fatty acid metabolites, and introduced a novel synthetic pathway for the biosynthesis of short-chain alkanes. This allowed the development of platform E. coli strain capable of producing gasoline for the first time. Furthermore, this platform strain, if desired, can be modified to produce other products such as short-chain fatty esters and short-chain fatty alcohols."

Find more at

http://www.youtube.com/watch?v=8KDXYMIgAi0

http://www.gbcghana.com/index.php?id=1.1550084

http://www.sciencedaily.com/releases/2013/09/130929142737.htm

Paper:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12536.html

Image source : Wikipedia