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  • Trevor M. Cickovski

  • Associate Professor of Computer Science at Eckerd College (On Leave 2015-2016), Visiting Professor of Computer Science at Florida International University (2015-2016)

  • Tenured: 2014

  • Office: ECS280D, Florida International University, Miami, FL 33196 (305) 348-8043

  • Home: 15265 SW 99th Ct, Miami, FL 33157 (574) 807-1965

  • Email: cickovtm@eckerd.edu, tcickovs@fiu.edu


Area(s) of expertise/research focus
Post-secondary education, GPU computing, social networks, computational biology/bioinformatics, molecular dynamics, domain-specific languages, software engineering
Education

Reverse chronological order



  • Ph.D, Computer Science and Engineering, University of Notre Dame, 2008

  • M.S., Computer Science and Engineering, University of Notre Dame, 2005

  • B.S., Computer Science, University of Notre Dame, 2002


Professional Experience

Reverse chronological order



  • Visiting Professor of Computer Science (2015-2016), Florida International University

    1. Four-course teaching load, office hours, collaboration with Bioinformatics Research Group (BioRG)

  • Associate Professor of Computer Science (2014-present, on leave 2015-2016), Assistant Professor (2008-2014) Eckerd College

    1. Seven-course teaching load, office hours, directing research projects, service to the college and community, mentoring

  • Research Assistant (2001-2008), University of Notre Dame

    1. Research projects in the field of computational science, including molecular dynamics, cellular automata and programming languages

  • Instructor (2007), University of Notre Dame

    1. Taught C/C++ Programming in the summer and fall semesters, office hours


Service to profession

  • Membership. American Association of University Professors (AAUP), Association for Computing Machinery (ACM), Interest Group on Simulation and Modeling (SIGPLAN), The Institute for Electrical and Electronics Engineers (IEEE)


Academic service

  • Leadership roles
    Discipline Coordinator, Department of Computer Science, Eckerd College (2012-2015)
    Reviewer, Journal of Computational Chemistry (2015)

Mentor, Computer Science Students (2009-present) and Freshman students (2010-2011) Chair, Admissions and Scholarships Committee, Eckerd College (2012-2013)
Chair, Computer Policy Group, Eckerd College (2010-2011)
Independent Study Supervisor, Biology and the Game of Life (Eli Peake, 2015)

Independent Study Supervisor, Bioinformatics (Kyle Kempton, 2014)

Freshman Research Associateship Mentor (Annie Rodgers, 2013-2014)

Independent Study Supervisor, Efficient Scientific Software (Jonathan Bryant, 2013) * J. Bryant and T. Cickovski. An Environment for Prototyping Molecular Dynamics on the GPU in Python. Florida Undergraduate Research Conference (FURC'14). Miami, FL 2014, poster.


Independent Study Supervisor, Molecular Dynamics Laboratory (Cameron Crowson, 2013)
Summer Internship For Credit, Web Applications (Cole Laddusaw, 2013)
Independent Study Supervisor, Data Structures (Tiffany Flor, 2012)
Senior Thesis Supervisor,A Case Study on BDD for a Classroom Application (Austin Vance,2012) * A. Vance and T. Cickovski. Narwhal: A Case Study on Developing a Classroom Application Using Behavior-Driven Development. FURC2012: Florida Undergraduate Research Conference, Deland, FL 2012, poster. Also AJUR Publication (see below).
Independent Study Supervisor, Behavior Driven Design by User Interfaces (Austin Vance, 2011)
Independent Study Supervisor, Engaging User Interfaces (Austin Vance, 2011)
Summer Internship For Credit, Mitto Mo Programmer (Austin Vance, 2011)
Independent Study Supervisor, A Molecular Dynamics GUI (Kristofer McEwing, 2010) * K. McEwing and T. Cickovski. MDInter: A Molecular Dynamics Graphical User Interface. Florida Statewide Student Research Symposium. Jacksonville, FL 2011, poster.

  • Standing committee memberships
    Intercollegiate Athletics Committee (2014-2015)

Graduate Fellowship Advisor (2013-2014)
Admissions and Scholarships Committee (2011-2013, chair 2012-2013)
Computer Policy Group (2009-2011, chair 2010-2011)

  • Ad hoc committees
    Senior Thesis Committees (Galen Irving-Sachs, 2015; Austin Vance, 2012, chair; RJ Nowling, 2010)
    Faculty Observer to Board of Trustees (Buildings and Grounds, 2011-2012)
    Harvard Medical School/Center for Human Genetic Research Selection Committee (2009-2015)
    Writing Portfolio Reviewer (every semester 2010-present, plus summer 2011)


Honors and awards

    1. Tenure and Promotion to Associate Professor (2014), Eckerd College

    2. OpenMM Visiting Scholars Program (2012), Stanford University

    3. Kaneb Award for Excellence in Teaching (2006), University of Notre Dame Department of Computer Science and Engineering

    4. Upsilon Pi Epsilon (2004), Computer Science Honor Society

    5. Tau Beta Pi (2001), Engineering Honor Society


Teaching

      1. CDA4101, Structured Computer Organization (FA15, SP16), Florida International University

      2. CDA3103, Fundamentals of Computer Systems (FA15, SP16), Florida International University

    1. CS420, Translators and Compilers (SP09, SP11, SP13), Eckerd College

    2. CS415, Computer Networks (SP10, SP12, SP15), Eckerd College

    3. CS411, Operating Systems (FA09), Eckerd College

    4. CS410, Computer Science Seminar (SP11, FA11, SP12, FA12, SP13, FA14), Eckerd College

    5. CS320, Programming Languages (FA08, SP10, FA11, SP14), Eckerd College

    6. CS310, Computer Architecture (FA08, FA10, FA12, FA14), Eckerd College (plus lab)

    7. CS221N,Data Structures(FA08,SP09,FA09,SP10, SP11,SP12,FA12,SP13,SP14),Eckerd College

    8. CS143, Introduction to Computer Science (FA14)

    9. CS143M, Introduction to Computer Science (FA11, SP12, FA12, SP15), Eckerd College

    10. CS143M, Introduction to Computer Science Lab (FA11, SP12, FA12, SP13), Eckerd College

    11. CS110M, Survey of Computing (FA09, FA13, SP14), Eckerd College

    12. NA207N, Biology and the Game of Life (SP09, FA13, SP15), Eckerd College (Honors in FA13)

    13. QFM, Quest For Meaning (FA13), Eckerd College

    14. WHGC, Western Heritage in a Global Context (FA10, SP11), Eckerd College

    15. Biology and the Game of Life (WT10 and AT10), Eckerd College

    16. Mathematical Patterns in Nature (WT14), Eckerd College

    17. CS233, Advanced Programming (SU07, FA07), University of Notre Dame


Publications/Creative works

* T. Cickovski, V. Aguiar-Pulido, W. Huang, S. Mahmoud and G. Narasimhan. Lightweight Microbiome Analysis Pipelines. Proceedings of International Work Conference on Bioinformatics and Biomedical Engineering (IWBBIO16), Granada, Spain, April 2016.

* V. Aguiar-Pulido, W. Huang, V. Ulloa-Suarez, T. Cickovski, K. Mathee and G. Narasimhan. Metagenomics, Metatranscriptomics and Metabolomics Approaches for Microbiome Analysis. Evolutionary Biology S(1):5-16, 2016.



* T. Cickovski, T. Flor, G. Irving-Sachs, P. Novikov, J. Parda and G. Narasimhan. GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on Graphics Processing Unit. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(2):445-454, 2015. * J. Sweet, R.J. Nowling, T. Cickovski, C.R. Sweet, V.S. Pande and J. A. Izaguirre. Long Timestep Molecular Dynamics on the Graphics Processing Unit. Journal of Chemical Theory and Computation 9(8) 3267-3281, 2013.
* A. Vance and T. Cickovski. A Case Study on Developing a Classroom Web Application Using Behavior Driven Development. American Journal of Undergraduate Research 11(3):9-16, 2012.
* G. Margolin, I.V. Gregoretti, T. Cickovski, C. Li, W. Shi, M.S. Alber and H.G. Goodson. The Mechanisms of Microtubule Catastrophe and Rescue: Implications From Analysis of a Dimer-Scale Computational Model. M. Biol. Cell 23(4):642-656, 2012.
* T. Cickovski, S. Chatterjee, J. Wenger, C. Sweet and J.A. Izaguirre. MDLab: A Molecular Dynamics Simulation Prototyping Environment. Journal of Computational Chemistry 31(7):1345-1356, 2010.
* T. Cickovski, K. Aras, M. Swat, R.M.H. Merks, T. Glimm, H.G.E. Hentschel, M.S. Alber, J.A. Glazier, S.A. Newman and J.A. Izaguirre. From Genes to Organisms via the Cell: A Problem Solving Environment for Multi-Cellular Development. Computing in Science and Engineering 9(4):50-60, 2007.
* T. Cickovski, C. Huang, R. Chaturvedi, T. Glimm, H.G.E. Hentschel, M.S. Alber, J.A. Glazier, S.A. Newman and J.A. Izaguirre. A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2(4):273-288, 2005.
* J.A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M.S. Alber, H.G.E. Hentschel, S.A. Newman and J.A.Glazier. CompuCell, A Multi-Model Framework for Simulation of Morphogenesis. Bioinformatics 20(7):1129-1137, 2004.
* T. Matthey, T. Cickovski, S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach and J.A. Izaguirre. ProtoMol, An Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics. ACM Transactions on Mathematical Software 20(3):237-265, 2004.

  • Other
    * R.J. Nowling and T. Cickovski. Prototype to Release: Software Engineering for Scientific Software. Biomedical Computation Review, Stanford University, Fall 2012.


Research/performance grants

    1. University of Maryland (equipment, 2016): Access to Data Intensive Academic Grid (DIAG)

    2. NVIDIA (equipment, 2016): Renewal of Eckerd College CUDA Teaching Center status. Received one high-performance TITAN graphics card plus teaching utilities

    3. Eckerd College ($6850, 2015): Natural Science Summer Research Program (NSSRP) grant to support two students for research projects

    4. Eckerd College ($2000, 2015): Faculty Development Grant to attend Florida Undergraduate Research Conference (FURC’15) at Embry-Riddle Aeronautical University, and perform research with the Bioinformatics Research Group (BioRG) at FIU

    5. Eckerd College ($9000, 2014): Natural Science Summer Research Program (NSSRP) grant to support three students for research projects

    6. Eckerd College ($2000, 2014): Faculty Development Grant to attend Florida Undergraduate Research Conference (FURC’14) at Florida International University, GPU Technology Conference in San Jose, CA and to perform research at Notre Dame Center for Research Computing (CRC)

    7. NVIDIA ($2000 plus equipment, 2013): Eckerd College officially named a CUDA Teaching Center. Received money to train a lab assistant to match funds for hiring the same assistant during the academic year. Also received four middle-tier GTX480 graphics cards for teaching GPU computing, and one high-performance Tesla graphics card for high-performance applications and demonstrating speed. Membership in the Center Rewards Program offers future discounts on equipment, also received a teaching kit with textbooks and other materials.

    8. Eckerd College ($7500, 2013): Natural Science Summer Research Program (NSSRP) grant to support three students for research projects

    9. Eckerd College ($2000, 2013): Faculty Development Grant to perform research at Notre Dame Center for Research Computing (CRC)

    10. Eckerd College ($5700, 2013): Natural Science Summer Research Program (NSSRP) grant to support two students for research projects, plus travel to Florida International University

    11. Eckerd College ($2000, 2012): Faculty Development Grant to perform research at Notre Dame Center for Research Computing (CRC)

    12. Eckerd College ($2000, 2011): Faculty Development Grant to perform research at Notre Dame Laboratory for Computational Life Sciences (LCLS)

    13. Eckerd College ($800, 2010): Faculty Development Grant to attend STEM Learning Conference in Miami, FL


Presentations, conferences

  • Invited presentations
    * T. Cickovski, E. Peake, V. Aguiar-Pulido and G. Narasimhan. ATria: A Novel Centrality Algorithm Applied to Biological Networks. Proceedings of 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS ‘15), Miami, FL, Oct. 2015.

* T. Cickovski, C. Sweet and J.A. Izaguirre. MDL, A Domain-Specific Language for Molecular Dynamics. Proceedings of IEEE 40th Annual Simulation Symposium, Norfolk, VA, March 2007.
* R. Chaturvedi, J.A. Izaguirre, C. Huang, T. Cickovski, P. Virtue, G. Thomas, G. Forgacs, M.S.Alber, H.G.E. Hentschel, S.A. Newman and J.A.Glazier. Multi-model Simulations of Chicken Limb Morphogenesis. In ICCS 2003, International Conference, Melboune, Australia and St. Petersburg, Russia. Lecture Notes Comput. Sci. 2659, pages 39-49, Springer-Verlag, 2003.

  • Other
    * H. Riggs, T. Cickovski and G. Narasimhan. Graphics Processing Unit Biofilm Image Processing (GPUBIP). Presented at Florida Undergraduate Research Conference (FURC2015), Embry-Riddle Aeronautical University, Deland, FL 2015, poster.

* T. Cickovski, T. Flor, G. Irving-Sachs, P. Novikov, J. Parda and G. Narasimhan. Hybrid Clustering Algorithms for Degenerate Primer Development on the GPU. GPU Technology Conference. San Jose, CA 2014, presentation.

* STEM Learning Conference, Miami, FL, 2010, participant.

* T. Cickovski. BioLogo Tutorial. CompuCell3D Workshop. Bloomington, IN 2007, presentation.
* T. Cickovski, C.R. Sweet and J.A. Izaguirre. MDLab Tutorial. IMA Classical and Quantum Approaches in Molecular Mechanics. Minneapolis, MN 2007, presentation.
* K. Aras, T. Cickovski, M. Swat, R.M.H. Merks, T. Glimm, H.G.E. Hentschel, M.S. Alber, J.A. Glazier, S.A. Newman and J.A. Izaguirre. CompuCell3D A Problem Solving Environment for Multicellular Development. Aritifical Life, Bloomington, IN 2006, poster.
* T. Cickovski and J.A. Izaguirre. Domain-Specific Languages in Computational Biology. Midwest Society for Programming Languages and Systems Meeting, Urbana, IL 2006.
* Midwest Molecular Dynamics Workshop, Notre Dame, IN, 2005, panelist.
* Biocomplexity VIII: Application of Methods of Stochastic Systems and Statistical Physics in Biology, Notre Dame, IN, 2005, session on CompuCell3D software, collaboration with Indiana University.
* T. Cickovski, R. Chaturvedi and J.A. Izaguirre. BioLogo: A Domain-Specific Language for Morphogenesis. SIAM Conference on Computational Science and Engineering, Orlando, FL 2005, presentation and session chair.
* T. Cickovski, R. Chaturvedi and J.A. Izaguirre. CompuCell: A Software Framework for Simulations of Morphogenesis. Biocomplexity VI: Complex Behavior in Unicellular Organisms, Bloomington, IN 2004, poster.
* T. Cickovski and J.A. Izaguirre. BioLogo: An XML-based Domain-Specific Language for Simulations of Morphogenesis. Biocomplexity IV: Regenerative Biology and Medicine, Bloomington, IN 2003, poster.
* T. Cickovski and J.A. Izaguirre. BioLogo: An XML-based Domain-Specific Language for Simulations of Morphogenesis. Midwest Numerical Analysis Day, Macomb, IL 2003, poster.

Other information


    1. Current Research Projects and Collaborations
      * Microbiome Analysis using Signatures for undocumented Microbes (MiAMi)

    2. Students: Lawrence Irvin and Cameron Davis (2015)

* ATria. A novel centrality algorithm for biological networks.

Students: Eli Peake (2015)

* GPUDePiCt (http://dantzig.eckerd.edu/gpudepict.htm). A software framework for constructing degenerate primers for aligned DNA sequences on the graphics processing unit (GPU).


Students: Tiffany Flor (2013), Galen Irving-Sachs (2013), Philippe Novikov (2012-2013), James Parda (2012)
* GPUBIP. A software framework for processing biofilm images and determining fractal dimension on the graphics processing unit (GPU). Students: Hugo Riggs (2014-2015), Kyle Kempton (2014) Collaboration: Giri Narasimhan and Bioinformatics Research Group (BioORG) at Florida International University

* Long Timestep Molecular Dynamics (https://github.com/LCLS/LTMDOpenMM). A plugin for the OpenMM software that can run simulations of molecular dynamics for longer biological periods of time using normal mode analysis, and executed on the graphics processing unit (GPU).


Students: Stephen Felman (2014)

Collaboration: Jesus Izaguirre and the Center for Research Computing (CRC) at Notre Dame, Vijay Pande and the NIH Center for Biomedical Computation at Stanford University.

* Molecular Dynamics Lab (http://mdlab.sourceforge.net). A Python environment for running molecular dynamics simulations, with GPU capability.


Students: Jonathan Bryant (2013-2014), Cameron Crowson (2013), Kristofer McEwing (2010)
Collaboration: Jesus Izaguirre and the Center for Research Computing (CRC) at Notre Dame.



    1. Past Research Projects and Collaborations
      * Narwhal (http://narwhal.iamaust.in). An interactive classroom tool developed as a case study for the software technique Behavior-Driven Design (BDD)
      Students: Austin Vance (2010-2012).

* CompuCell3D (http://www.compucell3d.org). A software framework that runs three-dimensional cell-centered simulations of morphogenesis


Collaboration: James Glazier and the Biocomplexity Institute at Indiana University (2002-2008).


    1. Miscellaneous Service
      * Service Project for Academy Prep Middle School, Alumni Database (http://www.academyprep.org/alumnidb) – with students in CS410 (Computer Science Seminar), (2012-2013)

* Wayside Baptist Church Handbell Choir (2015-present)

* Miami Vineyard Community Church Worship Team (2015-present)


* Laboratory Instruction (FA08, FA10, FA11, SP12, FA12, SP13, FA14)

* Living the Legacy Youth Ministry, Miami, FL (2008-2013)


* St. Mary Catholic Choir, St. Petersburg, FL (2011)
* Eckerd College Bible Study (2011)
* Eckerd College Africa Initiative (2009-2010)
* Eckerd College Praise and Worship Band (2009-2010)


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