User:Julius B. Lucks
I am a Miller Fellow at the University of California, Berkeley. With Adam Arkin, I am working on developing genetic systems that compute. I am also part of the arXiv.org project, where I am the lead developer of the applications programming interface.
Research/Projects
As a recent Miller Fellow, I have become interested in studying and developing biological cells that can perform programmable computations. While I don't think cellular based computing can rival the speed of silicon computing, I do believe that a cellular system that can be programmed is an extremely powerful tool for applications we can only begin to imagine.
In addition to scientific research, I am involved in projects aimed at improving the general science landscape.
- With Lorrie LeJeune, I helped to start OpenWetWare's Open Writing Projects. As a first article, I have written an introduction to the Python programming language for scientists - Python, All A Scientist Needs.
- I am also the lead developer of the arXiv.org API, which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at arXiv.org. The API allows software developers to include arXiv.org information, thereby giving scientists easy to use tools to access scientific literature.
Interests
In addition to science, I am becoming more and more fascinated with how the internet can be used to make some of the common tasks in science more efficient. I enjoy thinking about topics such as:
- How to make the literature system more efficient through better user interfaces to searching. One of the main reasons for opening up the arXiv via an API is to allow the creation of better search interface tools - now its up to you to try out some crazy ideas!
- Low-overhead customizable databases for quick and flexible organization of data. If you are interested in this topic, please add your comments to OpenWetWare:Software/Flexible_Science_Databases.
- Using the internet for fast publication of results.
- Broad community ranking of the usefulness/integrity of such results.
I recently started a project (with the same group of friends) making a game for the $100 Laptop as part of the One Laptop Per Child Project. The game is a generalization of classic Number Munchers, with question content derived from a whole range of topics including learning numbers, arithmetic, spelling, vocabulary, you name it!
Tools I Like
Python - I used to use a lot of different languages for all my tasks, but now I consider Python as my one-stop-shop. I do all sorts of stuff, from serious number crunching to making plots to scripting in it. I firmly believe that python is the best scientific programming platform out there.
I have always wanted to write a series of articles on great scientific tools. I have started one, Scientific Pipelines, that I hope turns into a nice resource for someone just entering into scientific programming.
Despite the languages listed above, I recently took the 'Which Programming Language Are You?' quiz, and found out that <html> <a href="http://www.bbspot.com/News/2006/08/language_quiz.php"><img src="http://www.bbspot.com/Images/News_Features/2006/08/language/lisp.jpg" width="300" height="90" border="0" alt="You are Lisp. Very few people like you (Probably because you use too many parenthesis (You better stop it (Reallly)))"><br>Which Programming Language are You?</a> </html> Lisp is awesome.
Inspiration
There are some really great thinkers out there ...
- Paul Graham's essays are fantastic. He has a lot to say about young people full of creative energy - from how they like to work, to common pitfalls they encounter. If any of you have a need to hear some advice from someone who understands the way you think and work, check these out. In particular I like:
OpenWetWare
Science
Research
My specific projects during graduate school have dealt with
- Unzipping DNA at a constant force
- Translocating RNA through nanopores
- Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
- Phage genome landscapes - a way to visualize important genomic features
My current research involves implementing computational architectures as genetic circuits inside cells.
Education
- Ph. D. in chemical physics at Harvard University.
- M. Phil. in theoretical physics at the CUC3 at Cambridge University (Churchill College).
- B.S. in chemistry (Math minor) at the University of North Carolina at Chapel Hill.
Publications
J. B. Lucks Python - All a Scientist Needs.
- OWW: Article Page (FREE)
- Arxiv: arXiv:0803.1838 (q-bio.QM) (FREE)
J. B. Lucks, D. R. Nelson, G. Kudla, J. B. Plotkin. Genome landscapes and bacteriophage codon usage, PLoS Computational Biology, 4, .1000001, 2008.
- DOI: 10.1371/journal.pcbi.1000001 (FREE)
- Arxiv: arXiv:0708.2038v1 (q-bio.GN) (FREE)
J. B. Lucks, Y. Kafri. Dynamics of RNA Translocation through a Nanopore.
- Arxiv: q-bio.BM/0703028 (FREE)
V. Vitelli, J. B. Lucks, D. R. Nelson. Crystallography on Curved Surfaces. PNAS, 103, 12323-12328, 2006.
- DOI: 10.1073/pnas.0602755103 (FREE)
- Arxiv: cond-mat/0604203 (FREE)
J. D. Weeks, J. B. Lucks, Y. Kafri, C. Danilowicz, D. R. Nelson and M. Prentiss. Pause Point Spectra in DNA Constant-Force Unzipping, Biophysical Journal, 88, 2752-2765, 2005.
- DOI: 10.1529/biophysj.104.047340,
- Arxiv: cond-mat/0406246 (FREE)
Contact
My email address is lucks at fas dot harvard dot edu, or you can email me through OWW.
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