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Using SNA for Mining Collaboration Data in a Bug Tracking System for Risk and Vulnerability Analysis
Ashish Sureka, Atul Goyal, Ayushi Rastogi

We derive a collaboration network from a defect tracking system and apply SNA techniques to investigate the derived network for the purpose of risk and vulnerability analysis. We demonstrate how important information pertaining to risk and vulnerability can be uncovered using network analysis techniques from static record keeping software archive such as the bug tracking system.

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Molecular Dynamics Study of Binary Mixture Lubricating Film in Hard Disk Interface
Purushothaman,K.,Anandan,N.

As distance between the HMS in HDD shrink,there is a need for usage of binary mixture lubricants to overcome the problem of retention and replenishment of lubricants on HDD surface. In this work, lubrication performance of binary mixture will be modelled using MD simulation based on a coarse-grain spring model using Euler Algorithm.

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Nucleic Acid Reagents and Experimental Results in the NCBI Probe Database
Svetlana Iazvovskaia, Ilene Karsch Mizrachi, Kirill Rotmistrovsky, and Savani Tatake

Five years ago, the NCBI Probe database (ProbeDB) was established to provide a centralized archive of molecular probes used in biomedical applications. Currently ProbeDB contains around 10 million probes of 65 types including gene silencing agents, in situ hybridization probes, and probes for variation analysis and genome mapping. Presently, ProbeDB is the largest and most extensive database of this type available in public domain.

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Enzyme kinetic measurements performed on BMG LABTECH´s FLUOstar OPTIMA

BMG LABTECH has developed a new evaluation software feature able to calculate the Km value as well as the maximal velocity (Vmax) from an enzymatic kinetic measurement. Enzymes differ in their affinity to specific substrates and this affinity is represented by the Michaelis-Menten constant Km. The new software feature for enzyme kinetic offers fast and easy calculation of Km and Vmax. Available plots are the common Michaelis-Menten, Lineweaver-Burk, Eadie-Hofstee, Scatchard and Hanes kinetic f

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Feasibility study through design and implementation of a web services based RFID solution
Arunabh Chattopadhyay

The implementation of an RFID solution based on web services is demonstrated. The solution has three components.

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Protein array-based screening of autoantibody signatures
Zingaretti C., Arigò M., Colombatto P., Brunetto M., Muratori L., Bonino F., Bianchi F., Pagani M., De Francesco R., Abrignani S., Bombaci M.

The evidence for an association between autoimmune diseases and chronic HCV infection has been clearly established. To this aim, a protein array was employed to analyze serum samples of HCV patients w/wo autoimmune complications, of patients with autoimmune hepatitis but not infected with HCV and of healthy donors as controls. A panel of autoantigens able to discriminate among the three groups of patients was identified for potential use as biomarkers.

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Software for Genomic/Epigenomic Research
A.S.Tanas, V.V.Shkarupo, E.B.Kuznetsova, D.V.Zaletayev, V.V. Strelnikov

We present two computer programs: 1) AIMS in silico - a suggestion tool for Amplification of Intermethylated Sites experimental design and results analysis; and 2) PeakPick – a tool to view & analyse capillary electrophoregrams Our computer software is intended to standardize AIMS applications and to turn it into one of the principal approaches towards cancer methylomes studies as well as towards diagnostics in oncology, including early screening.

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Geneset-based cancer survival analysis: On the non-uniform distributiuon of p-values under the null hypothesis
Esteban Czwan, Benedikt Brors, David Kipling

Although null p-values are assumed to be uniformly distributed in gene expression experiments, the actual distribution often deviates from the assumed distribution. This can incorrectly associate the biology of a geneset with cancer prognosis in geneset-based survival studies. To assess the implications of this, a geneset-based method was developed. This method empirically approximates the distribution of null p-values and tests whether predefined sets of biologically-related genes are associate

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Homology modeling and docking studies of Comamonas testosteroni B-356 biphenyl-2, 3-dioxygenase involved in degradation of polychlorinated biphenyls
M. Saqib Baig and N. Manickam

The three-dimensional model of a-subunit of Biphenyl dioxygenase (BphA) from Comamonas testosteroni B-356 has been constructed. The kinetic parameters of biphenyl compounds were well matched with the docking results. The binding properties of these biphenyl compounds along with identification of critical active site residues could be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity.

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Scientific News
Advancing Protein Visualization
Cryo-EM methods can determine structures of small proteins bound to potential drug candidates.
Gene Expression Controls Revealed
Researchers have modelled every atom in a key part of the process for switching on genes, revealing a whole new area for potential drug targets.
Making Genetic Data Easier to Search
Scripps team streamlines biomedical research by making genetic data easier to search.
Monovar Drills Down Into Cancer Genome
Rice, MD Anderson develop program to ID mutations in single cancer cells.
It’s Now Easier To Go With The Flow
Rice University tool simplifies comparison of flow cytometry data for laboratories.
Making Precision Medicine a Reality
Researchers are one step closer to understanding the genetic and biological basis of diseases like cancer, diabetes, Alzheimer’s and rheumatoid arthritis – and identifying new drug targets and therapies.
New Database for Sharing MS Clinical Trial Data
A new database containing nearly 2500 patient records from the placebo arms of nine multiple sclerosis (MS) clinical trials is now available for research by qualified investigators.
‘Precision Prevention’ for Colorectal Cancer
New risk prediction model — not yet ready for clinical use — incorporates genetic, lifestyle and environmental risk factors.
Characterizing Cancerous Genomic Variations
Tested on large tumor genomics database, REVEALER method allows researchers to connect genomics to cell function.
Uncovering Hidden Genomic Alterations that Drive Cancers
Tested on large tumor genomics database, REVEALER method allows researchers to connect genomics to cell function.
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