Book

Genetic Design Automation: A Practical Approach for the Analysis, Verification and Synthesis of Genetic Logic Circuits

Smiley face This book is intended for a multi-disciplinary audience of computer scientists, engineers and biologists. It provides enough background knowledge for computer scientists and engineers, who usually do not have any background in biology but are interested to get involved in this domain. This book not only presents an accessible basic introduction to molecular biology, it also includes software tools which allow users to perform laboratory experiments in a virtual in-silico environment. This helps newbies to get a quick start in understanding and developing genetic design automation tools.

The third part of this book is particularly useful for biologists who usually find it difficult to grasp programming and are reluctant to developing computer software. They are introduced to the graphical programming language, LabVIEW, from which they can start developing computer programs rapidly. Readers are further provided with small projects which will help them to start developing GDA tools. Chapters are followed by exercises which give readers a hands-on practice with the tools presented. The concepts and algorithms are thoroughly described, enabling readers to improve the tools or use them as a starting point to develop new tools. Both DVASim and GeneTech are available to download from http://bda.compute.dtu.dk/, free of charge.

Patents

International

Self-Repairing Fault-Tolerant FPGA Computation Unit and Architecture

Inventor: Hasan Baig and Jeong-A Lee.
US Patent 9720766.
Issued on August 01, 2017.

Provisional / Domestic

Programmable platform for testing and prototyping genetic logic circuits

Inventor: Hasan Baig
Application #: 6324****.
Filed on Sept. 15, 2021.

Bio-inspired Fault-Tolerant FPGA Computation Cell

Inventor: Hasan Baig and Jeong-A Lee.
Korea Registration Number: 101279999.
Issued on June 24, 2013.

Self-Repairing Bio-inspired Fault-tolerant FPGA

Inventor: Hasan Baig and Jeong-A Lee
Korea Registration Number: 101400809.
Issued on May 22, 2014.

Research Publications

Dissertations

PhD (Computer Science - worked on Genetic Design Automation)
Title: Methods and Tools for the Analysis, Verification and Synthesis of Genetic Logic Circuits.

MS (Computer Engineering - worked on embedded systems)
Title: A Self-Repairing Bio-Inspired Fault-Tolerant FPGA Architecture.

BE (Electronic Engineering - worked on embedded systems)
Title: Development and Verification of Soft IP Core of USB 3.0 in Verilog HDL.
Note: This was a group project of four students (including me) in which my contributions are the development of PHY/MAC layer controller and Master controller of USB 3.0 device.

Journals

  1. Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Chris Myers, et al. “Synthetic Biology Open Language visual (SBOL visual) version 3.0”, Journal of Integrative Bioinformatics, October, 2021.

  2. Sanaullah, Hasan Baig, Jan Madsen, Jeong-A Lee, “A parallel approach to perform threshold value and propagation delay analyses of genetic logic circuit models”. (Accepted in ACS Synthetic Biology)

  3. Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Chris Myers, et al. “Synthetic Biology Open Language visual (SBOL visual) version 2.2”, Journal of Integrative Bioinformatics, June 10, 2020.

  4. Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Chris Myers, et al., “Synthetic Biology Open Language (SBOL) version 3.0.0”, Journal of Integrative Bioinformatics, April 2020.

  5. Hasan Baig and Jan Madsen, “Simulation Approach for Timing Analysis of Genetic Logic Circuits”, ACS Synthetic Biology, January 19, 2017.

  6. Hasan Baig and Jan Madsen, “D-VASim - An Interactive Virtual Laboratory Environment for the Simulation and Analysis of Genetic Circuits”, Bioinformatics, September 11, 2016.

  7. Hasan Baig, Jeong-A Lee and Zahid Ali Siddiqui, “A Low-overhead Multiple-SEU Mitigation Approach for SRAM-based FPGAs with Increased Reliability”, IEEE Transactions on Nuclear Sciences, Vol. 61, Issue 3, pp 1389-1399, May 14 2014.

  8. Hasan Baig, Muhammad Asrar Alam and Jeong-A Lee, “Integrated LTSSM (Link Training & Status State Machine) and MAC Layer of USB 3.0 Device for Reliable SuperSpeed Data Transactions”, Research Notes in Information Sciences (RNIS), Vol. 9, pp. 37-47, ISSN 2093-1956, May 2012.

  9. Hasan Baig and Jeong-A Lee, “Architectural Development and Functional Verification of SuperSpeed USB 3.0 PHY Layer Controller”, Journal of Computing, Vol. 3, Issue 5, pp. 1-12, ISSN 2151-9617, May 2011.

Book Chapters

  1. Hasan Baig and Jan Madsen, “Taming Living Logic using Formal Methods”, Models, Algorithms, Logics and Tools, Lecture Notes in Computer Science (LNCS), vol. 10460, Springer, 2017.

  2. Hasan Baig, Jeong-Gun Lee and Jeong-A Lee, “A Novel Automated Experimental Approach for the Measurement of On-Chip Speed Variations through Dynamic Partial Reconfiguration”, Advances in Automation and Robotics, LNEE 123, Vol. 2, pp. 281-290, Springer, 2011.

Conferences and Workshops

  1. Sanaullah, Hasan Baig, Jeong-A Lee, “Accelerating the Threshold and Timing Analysis of Genetic Logic Circuit Models”, 11th IWBDA 2019, Cambridge, England, July 08 - 10, 2019.

  2. M. Abdullah Siddiqui, Adil Ali Khan, Hasan Baig, Jan Madsen, “GeneTech 2.0: Improved Genetic Circuit Synthesis and Technology Mapping”, 10th IWBDA 2018, Berkeley, CA, USA, July 31 - Aug 03, 2018.

  3. Hasan Baig and Jan Madsen, “A Top-down Approach to Genetic Circuit Synthesis and Optimized Technology Mapping”, 9th International Workshop on Bio Design Automation (IWBDA), pp. 28-29, 2017.

  4. Hasan Baig and Jan Madsen, “Logic Analysis and Verification of n-input Genetic Logic Circuits”, Design Automation and Test in Europe (DATE), March 27-31, 2017.

  5. Hasan Baig and Jan Madsen, “Logic and Timing Analysis of Genetic Logic Circuits using D-VASim”, 8th International Workshop on Bio Design Automation (IWBDA) 2016, Newcastle upon Tyne, UK, August 16-18, 2016.

  6. Hasan Baig and Jan Madsen, “D-VASim: Dynamic Virtual Analyzer and Simulator for Genetic Circuits”, 7th International Workshop on Bio-Design Automation (IWBDA) 2015, Seattle Washington, USA, Aug 19-21, 2015.

  7. Hasan Baig and Jeong-A Lee, “An Island-style-routing Compatible Fault-Tolerant FPGA Architecture with Self-Repairing Capabilities”, Field Programmable Technology (FPT) 2012, pp 301-304 (ISBN: 978-1-4673-2846-3), Seoul, South Korea, Dec. 10-12, 2012.

  8. Hasan Baig, Jeong-A Lee and Jieun Lee, “Performance Evaluation of CPU-GPU and CPU-only Algorithms for Detecting Defective Tablets through Morphological Imaging Techniques”, CISTI 12, IEEE Vol. 2, pp. 1-6 (ISBN: 978-1-4673-2843-2), ISI Web of Knowledge, Vol. 1-2, pp. 568-573 (ISBN: 978-989-96247-6-4), Spain, June 20-23, 2012.

  9. Hasan Baig and Jeong-A Lee, “Implementation and Functional Verification of Soft IP Core of USB 3.0 Device MAC Layer”, Proceedings of the International Conference on Embedded Systems and Applications (ESA'11), pp. 158-164, ISBN: 1-60132-178-3, Las Vegas, Nevada, USA, July 18-21, 2011.

  10. Hasan Baig, M. Mansoor Ikram, Kamran Shamim, Ahmed Taha Akbar and Ahmed Hassan, “Implementation of SCADA System for Unsought Tablets Detection through Morphological Image Processing”, 12th IEEE International Multi Topic Conference (IEEE INMIC 2008), pp. 493-500, ISBN: 978-1-4244-2824-6, December 23-24, 2008.

  11. Hasan Baig, M. Owais, M. Saleheen Aftab, Kamran Shamim & Hamza Azeem, “GSM Based Security System Using LabVIEW”, Proceedings First International Conference on Computer, Control and Communication, PNEC Karachi, November 12-13, 2007.

Posters and Project Demonstrations

  1. Hasan Baig and Jan Madsen, “Timing Analysis of Genetic Logic Circuits using D-VASim”, University Booth at Design Automation and Test in Europe (DATE) 2016, Dresden, Germany, Mar 15-17, 2016.
  2. Hasan Baig and Jan Madsen, “Analysis and Verification of Genetic Logic Circuits using D-VASim”, Synthetic and Systems Biology Summer School (SSBSS) 2015, Taormina, Italy, July 5-9, 2015.
  3. Hasan Baig and Jeong-A Lee, “A Self-repairing Bio-inspired Fault-Tolerant FPGA Architecture”, 25th ACM SIGDA University Booth and ACM SRC, 49th Design Automation Conference (DAC), San Francisco, USA, Jun 3-7, 2012.
  4. Hasan Baig and Jeong-A Lee, “A Novel Run-time Auto-Reconfigurable FPGA Architecture for Fast Fault-Recovery with Backward Compatibility”, 21st ACM/SIGDA International Symposium on Field Programmable Gate Arrays, Monterey California, February 12, 2013.

Reports Published by Industries

  1. D-VASim: A Software Tool to Simulate and Analyze Genetic Logic Circuits, published by National Instruments and can be seen here.

Domestic Magazines

  1. Hasan Baig, “Low Cost Fabrication of Highly Reliable Single-Sided PCBs”, SPARK, Annual Magazine of Electronic Department, NED University of Engineering & Technology, Karachi, Pakistan, August 2007.