Personal data

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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)
  
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  Tenured: 2014
  
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  Office: ECS280D, Florida International University, Miami, FL 33196 (305) 348-8043
  
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  Home: 15265 SW 99th Ct, Miami, FL 33157 (574) 807-1965
  
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  Email: cickovtm@eckerd.edu, tcickovs@fiu.edu
  

Reverse chronological order

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  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
  

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
     
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  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
     
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  Instructor (2007), University of Notre Dame
  
  1. 
     Taught C/C++ Programming in the summer and fall semesters, office hours
     

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  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)
  

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

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  Standing committee memberships
  Intercollegiate Athletics Committee (2014-2015)
  

• 
  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)
  

2. 
   Tenure and Promotion to Associate Professor (2014), Eckerd College
   
3. 
   OpenMM Visiting Scholars Program (2012), Stanford University
   
4. 
   Kaneb Award for Excellence in Teaching (2006), University of Notre Dame Department of Computer Science and Engineering
   
5. 
   Upsilon Pi Epsilon (2004), Computer Science Honor Society
   
6. 
   Tau Beta Pi (2001), Engineering Honor Society
   

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
    

• 
  Peer reviewed articles, chapters, exhibitions, productions:
  

* 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.

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

24. 
    University of Maryland (equipment, 2016): Access to Data Intensive Academic Grid (DIAG)
    
25. 
    NVIDIA (equipment, 2016): Renewal of Eckerd College CUDA Teaching Center status. Received one high-performance TITAN graphics card plus teaching utilities
    
26. 
    Eckerd College ($6850, 2015): Natural Science Summer Research Program (NSSRP) grant to support two students for research projects
    
27. 
    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
    
28. 
    Eckerd College ($9000, 2014): Natural Science Summer Research Program (NSSRP) grant to support three students for research projects
    
29. 
    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)
    
30. 
    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.
    
31. 
    Eckerd College ($7500, 2013): Natural Science Summer Research Program (NSSRP) grant to support three students for research projects
    
32. 
    Eckerd College ($2000, 2013): Faculty Development Grant to perform research at Notre Dame Center for Research Computing (CRC)
    
33. 
    Eckerd College ($5700, 2013): Natural Science Summer Research Program (NSSRP) grant to support two students for research projects, plus travel to Florida International University
    
34. 
    Eckerd College ($2000, 2012): Faculty Development Grant to perform research at Notre Dame Center for Research Computing (CRC)
    
35. 
    Eckerd College ($2000, 2011): Faculty Development Grant to perform research at Notre Dame Laboratory for Computational Life Sciences (LCLS)
    
36. 
    Eckerd College ($800, 2010): Faculty Development Grant to attend STEM Learning Conference in Miami, FL
    

• 
  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.
  

• 
  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.
  

* 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

37. 
    Current Research Projects and Collaborations
    * Microbiome Analysis using Signatures for undocumented Microbes (MiAMi)
    
38. 
    Students: Lawrence Irvin and Cameron Davis (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).

* 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).

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

39. 
    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

40. 
    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)
    

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

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