Preetam Ghosh

Address:                                                                                    

412, South Cooper St, Apt #69, Arlington, TX-76013,            

Department of Computer Science & Engineering,                     

University of Texas at Arlington.                                              

Contact Details:  

 Ph: 817-714-7295  

Email: preetam.ghosh@gmail.com

 Website: http://crewman.uta.edu/~preetam/

RESEARCH SUMMARY:

RESEARCH INTERESTS: 

§        Areas: Systems/Computational Biology, Bioinformatics, Models from Biophysics and Biochemistry, Distributed Computing, Wireless/Mobile Computing, Optical Networks.

 §         Skills: Stochastic modeling techniques, ODE/PDE based modeling, Discrete event simulation, Monte Carlo Simulation, Bioinformatics tools (e.g., TIP-EVE, Pharmamatrix, Ingenuity Pathway Analysis), Sitesorter, Siteseeker and Sequence Alignment algorithms, SimBiology toolkit of Matlab and Dizzy software developed by Institute for Systems Biology (Seattle), Linear/Non-linear Optimization techniques, Applications of game theory/queueing theory/scheduling theory/control theory/collision theory/graph theory/differential equations.

   
EDUCATION:

 

PhD in Computer Science & Engineering, University of Texas at Arlington: Sep, 2004 – Dec, 2007

· Stochastic models for In-Silico Event-based Biological Network Simulation.

Advisor: Dr. Sajal K Das and Mr. Kalyan Basu.

Date: December 2007.

 MS in Computer Science & Engineering, University of Texas at Arlington.  Sep, 2002 – Aug, 2004.

· An Optical Burst Switched (OBS) Transport Network to Support Long-Haul Traffic at the Core.

Advisor: Dr. Sajal K Das and Mr. Kalyan Basu.

Graduation Date: August 2004.

Bachelor in Computer Science & Engineering, Jadavpur University, Kolkata, INDIA.  July, 1996 – June 2000

· Design, implementation and testing of the Indian Language Interface With Database (ILID) Software: involving VC++ and Microsoft Access database concepts.

Advisor: Dr.Shibaji Bannerjee, Jadavpur University.
Graduation Date: June 2000.

PROFESSIONAL EXPERIENCE:

Industry Experience:

Exploratory Medicinal Sciences-Computational Biology Intern, June 2007 – Aug 2007

        Worked on automating the pocket mining activity by integrating bioinformatics tools (e.g., TIP-EVE, Pharmamatrix, Ingenuity Pathway Analysis) for drug target discovery using PERL, mySQL and C++. This initiated the TIP integration of the Pfizer internal protein database project where we store the publicly available and Pfizer proprietary proteins in a complex ORACLE database and fire SQL queries (using PERL scripts) to generate pdb files against specific PDB-Ids or protein sequences. We next applied the Sitesorter, Siteseeker and Sequence Alignment algorithms (C++ source code developed by Eidogen-Sertanty) for various pocket-mining activities e.g., pathway/target identification. The basic algorithms had to be tweaked to meet Pfizer’s target identification criteria. 

        Also worked on a systems biology project for the RNA interference (RNAi) system using the Gillespie Stochastic Simulator and ODE based simulators (from the SimBiology toolkit of Matlab and Dizzy software developed by Institute for Systems Biology, Seattle) for in silico prediction of the potency effects of siRNAs.

       

Wireless Core Systems Engineering Intern, Feb 2006 – May 2006

 Worked on data sanity checking for Large office testing of PMSC13 and proposing new KPIs (Key Performance indicators) for voice quality improvement in Nortel switches. Also worked on a novel overload control algorithm for revenue maximization in wireless switches and performance analysis for the CSCF based IMS subsystem for Nortel’s converged core network.

Research Intern, June 2004 – August 2004

 Propose and implement enhancements on existing Snap architecture to support massively multiplayer online networked games on wireless devices. This include changes in the gaming architecture (a hybrid of peer-to-peer and client-server architectures), identifying an efficient decentralized load balancer, modifying the transport layer protocols (RUDP) for efficient and reliable delivery of game packets, and proposing efficient algorithms for synchronization and fairness issues.  

Worked on a Real Time Kernel development for Embedded Systems applications.

 

Academic Experience:

1)       Post-doctoral Research Associate at UT Southwestern Medical Center (January, 2008 - till present):                                        

Advisor: Dr. Richard Scheuermann, Department of Pathology and Biomedical Informatics: Will be working on pathway/network modeling related projects for influenza infection in the Bioinformatics Lab.

 2)       Research Assistant at CreWMaN lab under Dr. Sajal Das and Mr. Kalyan Basu (Fall 2005): Worked on developing an analytical tool for performance evaluation and capacity planning of Nortel’s IP Multimedia Systems (IMS) that can reduce the complexity of OPNET based modeling in complicated server architectures. The work considered Intel’s blade server architecture on which Nortel is implementing the Java based Call Server Control Functions (CSCFs) of the IMS.

3)     Teaching Assistant: primarily related to C/C++ programming and algorithms/datastructures based courses:

       CSE 2320: Datastructures & Algorithms

      CSE 1320: C/C++ programming

       CSE 3315: Digital Logic & Programming

      CSE 5311: Advanced Algorithms

      CSE 3320/CSE 5351: Senior level Operating Systems and graduate level Parallel Processing (using MPI)

      

TECHNICAL SKILLS:

 ·         Programming Platforms & Languages: C, C++, Java, PERL, SQL, ORACLE, Assembly Languages (8085/8086/), HP-UX (10.XX & 9.XX), VxWorks, DSP-BIOS (in-built kernel for TMS320C54X processor).

 ·         Tools/Databases: Dizzy, Matlab, SQL-PLUS, My SQL Query Browser, ORACLE, TIP-EVE, Pharmamatrix, Ingenuity Pathway Analysis, BLAST, ClustalW, FASTA, PROSITE, Pfam, PDB, Entrez, KEGG, ECOCYC, XPPAUT, R statistical package, OPNET/NS-2, Globus toolkit.

 

PUBLICATIONS (Peer Reviewed): (Journals: J*, Book Chapters: B*, Conferences: C*, Posters/Extended Abstracts: P*)

 Book Chapters:

 Research Area:  Systems Biology

  1. Samik Ghosh, A. R Mazloom, Preetam Ghosh, Kalyan Basu, Sajal Das, Stochastic simulation of cellular dynamics: A Discrete Event based Approach, book chapter accepted for review at Springer-Verlag series in "Studies in Computational Intelligence", Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems (vol. 2), 2007.

Journals:

Research Area:  Systems Biology

  1. Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal Das, Holding Time Estimation for Reactions in Stochastic Event-based Simulation of Complex Biological Systems, to appear at Elsevier Simulation Modelling Practice and Theory, 2007.
  2. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daeffler, A Computationally Fast and Parametric Model to estimate Protein-Ligand Docking time for Stochastic Event based Simulation, to appear at LNCS Transactions on Computational Systems Biology, 2007.
  3. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daeffler, Parametric modeling of protein-DNA binding kinetics: A Discrete Event based Simulation approach, to appear at Journal of Discrete Applied Mathematics, special issue on Networks in Computational Biology.
  4. Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal Das and Simon Daeffler, A stochastic discrete event simulation approach to study system level dynamics of biological processes, under review
  5. Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal Das, Capturing the stochasticity in prokaryotic gene expression: A Birth and Death Markov Chain Approach, journal paper under review at IEEE/ACM Transactions in Computational Biology and Bioinformatics, 2007.

Research Area:  Distributed Computing

  1. Preetam Ghosh, Nirmalya Roy, Sajal Das and Kalyan Basu, A Pricing Strategy for Job Allocation in Mobile Grids using a Non-cooperative bargaining Theory Framework, in Special Issue on Design and Performance of Networks for Super-Cluster and Grid-Computing, JPDC, 2005, Volume 65, Issue 11, pp. 1366-1383.
  2. Preetam Ghosh, Kalyan Basu and Sajal Das, A Game Theory based Pricing Strategy to support Single/Multi-Class Job Allocation Schemes for Bandwidth Constrained Distributed Systems. IEEE Transactions on Parallel and Distributed Systems, 2007, Volume 18, Issue 3, pp. 289-306

Research Area:  Optical Networks

  1. Preetam Ghosh, Kalyan Basu and Sajal Das, A Novel Photonic Container Switched Architecture and Scheduler to Design the Core Transport Network. IEEE Transactions on Computers, 2007, Volume 56, Issue 8, pp. 1087-1104.
  2. Amin R Mazloom, Preetam Ghosh, Kalyan Basu and Sajal Das, CoCONet: A Collision-free Container-based Core Optical Network, to appear at Elsevier Computer Networks Journal.

Research Area:  Optimization problems in Wireless Networks

  1. Preetam Ghosh, Kalyan Basu and Sajal Das, Improving End-to-End Quality of Service in Online Multiplayer Wireless Gaming Networks. To appear at Elsevier Computer Communications, special issue on End-to-end Support over Heterogeneous Wired-Wireless Networks.
  2. Haitao Lin, Preetam Ghosh and Prabir Das, Wireless Networks Revenue Optimization through Overload Control with Priority Services, in the Journal of Communications (JCM), issue 4, 2006, Volume 1, Issue 4, pp. 22-30.

Conferences:

Research Area:  Systems Biology

  1. Samik Ghosh, Preetam Ghosh, Kalyan Basu, S. Daefler and S. Das, “iSimBioSys: A Discrete Event Simulation Platform for 'in silico' Study of Biological Systems”, IEEE 39th Annual Simulation Symposium, 2006 pp. 204-213.
  2. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler, "An Analytical Model to Estimate the time taken for Cytoplasmic Reactions for Stochastic Simulation of Complex Biological Systems", IEEE Granular Computing Conference, 2006, pp. 79-84.
  3. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler, "Stochastic Modeling of Cytoplasmic Reactions in Complex Biological Systems", International Conference on Computational Science and its Applications, ICCSA 2006, pp. 566-576.
  4. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler, "Modeling the Diffusion process in Stochastic Event based Simulation of the PhoPQ system", International Symposium on Computational Biology and Bioinformatics (ISBB 2006), December, 2006, Bhubaneshwar, India, pp. 1-6.
  5. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler. Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2007, Hawaii, USA, pp. 439-446.
  6. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler. A stochastic model to estimate the time taken for protein-ligand docking. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2006, Toronto, Canada, pp. 1-8.
  7. Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal K Das, A Markov Model based Analysis of Stochastic Biochemical Systems. LSS Computational Systems Bioinformatics Conference (CSB) 2007, pp. 121-132.
  8. Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal K Das, Modeling the stochastic dynamics of gene expression in single cells: A Birth and Death Markov Chain Analysis. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2007.
  9. Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal K Das, Modeling the stochastic dynamics of
    protein synthesis: A discrete event simulation approach. Biotechnology and Bioinformatics Symposium (BIOT-2007), Colorado Springs, 2007.

Research Area:  Distributed Computing

  1. Preetam Ghosh, Nirmalya Roy, Sajal Das and Kalyan Basu, A Game Theory based Pricing Strategy for Job allocation in Mobile Grids. 18th IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2004, USA, pp. 82-91.
  2. Preetam Ghosh, Kalyan Basu and Sajal Das, Cost-Optimal Job Allocation Schemes for Bandwidth-Constrained Distributed Computing Systems. 12th Annual IEEE International Conference on High Performance Computing (HiPC), 2005, Goa, India, pp. 40-50.
  3. Preetam Ghosh, Nirmalya Roy and Sajal Das, Mobility-based Cost-efficient Job Scheduling in Mobile grids. 1st IEEE International Workshop on Context-Awareness and Mobility in Grid Computing (held in conjunction with CCGrid 2007), 2007, Brazil, pp. 701-706.

Research Area:  Optical Networks  

  1. Preetam Ghosh, Kalyan Basu and Sajal Das, A Novel Photonic Container Switched OBS Architecture and Nonpreemptive Scheduler for the Core Transport Network. 19th International Teletraffic Congress (ITC19), 2005, China, pp. 1-10.
  2. Preetam Ghosh, Kalyan Basu and Sajal Das, A Photonic Container Switched Transport Network to Support Long-Haul Traffic at the Core. Second IEEE International Conference on Broadband Networks (Broadnets Optical networking Symposium), 2005, Boston, USA, pp. 104-113.
  3. Preetam Ghosh, Amin R Mazloom, Kalyan Basu and Sajal K Das: A Centrally-Scheduled Photonic Container Switched Architecture For The Core Transport Network. Pacific Telecommunication Council Conference, 2006, Hawaii, USA, pp. 1-17.

Research Area:  Optimization problems in Wireless Networks

  1. Preetam Ghosh, Kalyan Basu and Sajal Das, A Cross-Layer Design to Improve Quality of Service in Online Multiplayer Wireless Gaming Networks. Second IEEE International Conference on Broadband Networks (Broadnets Applications/Services Symposium), 2005, Boston, USA, pp. 875-884.
  2. Preetam Ghosh, Nirmalya Roy, Kalyan Basu, Sajal K Das, Paul Wilson and Prabir Das: A Case Study-based Performance Evaluation Framework for CSCF Processes on a Blade-Server. 3rd IEEE International Conference on Networking and Services, Greece, 2007, pp. 87-96.
  3. Soumya Sanyal, Preetam Ghosh, Kalyan Basu and Sajal Das, Towards the Optimal design of an Enterprise Network: A genetic algorithm perspective. XVth International Symposium on Services and Local Access (ISSLS), 2004, UK, pp. 1-7.
  4. Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal Das, GaMa: An Evolutionary Algorithmic Approach for the Design of Mesh-Based Radio Access Networks. 30th IEEE Conference on Local Computer Networks (LCN), 2005, Sydney, pp. 374-381.
  5. Sourav Pal, Preetam Ghosh, Sumantra R. Kundu, Amin Mazloom and Sajal K. Das, Two Phase Scheduling Algorithm for Maximizing the Number of Satisfied Users in Multi-Rate Wireless Systems. IEEE International Symposium on a World of Wireless, Mobile and Multimedia Networks (WOWMOM 2007), Finland, pp. 1-9.

Posters/Extended Abstracts:

Research Area:  Systems Biology

  1. Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal K Das, A Diffusion Model to Estimate the Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks. (poster paper) IEEE Computational Systems Bioinformatics Conference (CSB) 2005, Stanford University, USA, pp. 19-21.
  2. Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal K Das, iSimBioSys: An `In Silico’ Discrete Event Simulation Framework for Modeling Biological Systems. (poster paper) IEEE Computational Systems Bioinformatics Conference (CSB) 2005, Stanford University, USA pp. 170-171.
  3. Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal K Das, A Hybrid Simulation Framework for genome scale study of molecular dynamics in Escherichia Coli. Seventh International Conference on Systems Biology (ICSB 2006), Oct 9-13, Japan.
  4. Kalyan Basu, Samik Ghosh, Preetam Ghosh and Sajal Das. Genome scale cell modeling using stochastic discrete event simulation. (poster paper) accepted for publication at the Conference on Stochastic Networks (SNC 2006), UIUC, 2006.
  5. Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal K Das, Parametric and Stochastic Modeling of Molecular Reactions in the Cell. (poster paper) Dallas Area Bioinformatics and Computational Biology Workshop (DABC) 2006, U.T. SouthWestern Medical Centre, USA.
  6. Samik Ghosh, A. R Mazloom, Preetam Ghosh, Kalyan Basu and Sajal K Das, Connecting the dots: An integrated database for studying cellular dynamics. Eighth International Conference on Systems Biology (ICSB), Oct 2007, USA.

TECHNICAL REPORTS (Non-Peer Reviewed):

1)       Preetam Ghosh, S. Ghosh, K. Basu, S. Das, S. Daefler, "Estimation of the holding Time for Cytoplasmic Reactions in Stochastic Event Based Modeling of Complex Biological Networks", TR CSE-2005-09.

2)       Preetam Ghosh, S. Ghosh, K. Basu, S. Das, S. Daefler, "Transient analysis of Diffusion for charged molecules to model the input process in a stochastic event based simulation framework for the PhoPQ signal transduction system ", TR CSE-2005-07.

3)       Preetam Ghosh, Shashikant Maheshwari and Giridhar Mandyam, A Dynamic Packetization Scheme to Improve Transport Layer Performance in Online Multiplayer Wireless Gaming. Technical Report, Nokia Research Centre, Irving, Dallas.

 

RELEVANT COURSES:

 Advanced Algorithms, Advanced Operating Systems, Graph Theory and Combinatorics, Telecommunications Network Design, Computational Geometry, Local Area Networks, Advanced Wireless Networks, Cross-Layer Optimization in Wireless Networks, Multi-Service Switching Architecture, Computer System Performance (with emphasis on Queueing Theory), Parallel Processing, Advanced Bioinformatics Database, Bioinformatics, Advanced Topics in Bioinformatics, Modeling Biological Networks, Advanced Biostatistics.

PRESENTATIONS:


PROFESSIONAL ACHIEVEMENTS/AFFILIATIONS:

 ·        Recipient of the Nokia sponsored Best Master’s thesis award for academic year 2003-2004.

·        2nd place in IDEAZ 2005, Graduate Research Competition, at UTA.

·        2nd prize in Pacific Telecommunication Council (PTC) essay prize competition 2005  http://www.ptc.org/resources/essay2005_winner.html

·        Recipient of the Who’s Who Among American Students Award, 2006.

·        Recipient of the University Scholar Award, 2007 at UTA.

·        Recipient of Dean’s Fellowship at UTA: Fall 2002 – till present.

·        Recipient of TxTec scholarship at UTA: Fall, 2004 – Summer 2006.

·        Recipient of the Nokia Scholarship: Fall 2004.

·        Recipient of Graduate Teaching Assistantship at UTA: Fall 2002 – Summer 2005, Fall 2006 - present.

·        Recipient of Graduate Research Assistantship at UTA: Fall 2005-Summer 2006.

·        Nominated for Tau-Beta-Pi, National Engineering Honor Society, Fall 2003, Fall 2005, Fall 2007

·        Reviewer of IEEE and ACM conferences and journals e.g. IEEE Transactions on Parallel and Distributed Systems, IEEE Transactions on Networking, IEEE Transactions on Computers, JSAC, JPDC, Elsevier Computer Networks, Elsevier Computer Communicaions, ISMB, INFOCOM, MOBICOM, IPDPS, ICON, LCN, BROADNETS, CCGRID, HiPC, ICDCN, WOWMOM, ITC etc.

·        Student Member, IEEE Computer Society, Life Sciences Society.

·        Recipient of National Scholarship and Merit Awards at both Secondary and Higher Secondary (Plus Two) Levels

 

References:
Available upon request

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