User:Julius B. Lucks

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[[Image:JBL.jpg|200px|left|Julius B. Lucks]]
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I am a [http://millerinstitute.berkeley.edu/ Miller Fellow] at the University of California, Berkeley. With [http://genomics.lbl.gov/People.html Adam Arkin], I am working on developing genetic systems that compute.  I am also part of the [http://arxiv.org arXiv.org] project, where I am the lead developer of the [http://export.arxiv.org/api_help applications programming interface].
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I am a [http://millerinstitute.berkeley.edu/ Miller Fellow] at the University of California, Berkeley. With [http://genomics.lbl.gov/People.html Adam Arkin], I am working on developing genetic systems that compute.  I am also part of the [http://arxiv.org arXiv.org] project, where I am the lead developer of the [http://export.arxiv.org/api_help applications programming interface].  You can reach me at jblucks at berkeley dot edu.
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In addition to scientific research, I am involved in projects aimed at improving the general science landscape.   
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|Open Writing Projects]].  As a first article, I have written an introduction to the Python programming language for scientists - [[Julius_B._Lucks/Projects/Python_All_A_Scientist_Needs|Python, All A Scientist Needs]].   
* With Lorrie LeJeune, I helped to start OpenWetWare's [[Open_writing_projects|Open Writing Projects]].  As a first article, I have written an introduction to the Python programming language for scientists - [[Julius_B._Lucks/Projects/Python_All_A_Scientist_Needs|Python, All A Scientist Needs]].   
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* I am also the lead developer of the [http://export.arxiv.org/api_help arXiv.org API], which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at [http://arxiv.org arXiv.org].  The API allows software developers to include arXiv.org information, thereby giving scientists easy to use tools to access scientific literature.
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* I am also the lead developer of the [http://export.arxiv.org/api_help arXiv.org API], which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at [http://arxiv.org arXiv.org].  The API allows software developers to include arXiv.org information, thereby giving scientists easy to use tools to access scientific literature.  It also paves the way for creative uses of the information, and the creation of better search interface tools.
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== Interests ==
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For my PhD, I worked in the area of biophysics with [http://www.physics.harvard.edu/people/facpages/nelson.html David Nelson], where we used theoretical physics to study problems related to
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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:
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*How to make the literature system more efficient through better user interfaces to searching.  One of the main reasons for opening up the [http://arxiv.org 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!
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*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]].
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*Using the internet for fast publication of results.
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**Broad community ranking of the usefulness/integrity of such results.
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I recently started a project (with the same group of friends) making a [http://wiki.laptop.org/go/Kuku game] for the [http://wiki.laptop.org/go/Image:Drawing75c1.jpg $100 Laptop] as part of the [http://wiki.laptop.org One Laptop Per Child Project].  The game is a generalization of classic [http://en.wikipedia.org/wiki/Number_Munchers Number Munchers], with question content derived from a whole range of topics including learning numbers, arithmetic, spelling, vocabulary, you name it!
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== Tools I Like ==
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'''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.
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I have always wanted to write a series of articles on great scientific tools.  I have started one, [[Lucks/Scientific_Pipelines|Scientific Pipelines]], that I hope turns into a nice resource for someone just entering into scientific programming.
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Despite the languages listed above, I recently took the 'Which Programming Language Are You?' quiz, and found out that
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<a href="http://www.bbspot.com/News/2006/08/language_quiz.php"><img
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src="http://www.bbspot.com/Images/News_Features/2006/08/language/lisp.jpg" width="300" height="90"
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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>
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Lisp is awesome.
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== Inspiration ==
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There are some really great thinkers out there ...
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* [http://www.paulgraham.com/articles.html 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:
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**[http://www.paulgraham.com/love.html How to do what you Love]
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**[http://www.paulgraham.com/procrastination.html Good and Bad Procrastination]
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**[http://www.paulgraham.com/bronze.html Why Smart People Have Bad Ideas]
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== OpenWetWare ==
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*[[Special:Contributions/Lucks | My Contributions]]
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== Science ==
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===Research ===
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My specific projects during graduate school have dealt with
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*Unzipping DNA at a constant force
*Unzipping DNA at a constant force
*Translocating RNA through nanopores
*Translocating RNA through nanopores
*Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
*Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
*Phage genome landscapes - a way to visualize important genomic features
*Phage genome landscapes - a way to visualize important genomic features
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My current research involves implementing computational architectures as genetic circuits inside cells.
 
=== Education ===
=== Education ===
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:Arxiv: [http://www.arxiv.org/abs/cond-mat/0406246 cond-mat/0406246] (FREE)
:Arxiv: [http://www.arxiv.org/abs/cond-mat/0406246 cond-mat/0406246] (FREE)
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== Contact ==
 
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My email address is lucks at fas dot harvard dot edu, or you can [[Special:Emailuser/Julius_B._Lucks|email me]] through OWW.
 
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Revision as of 00:51, 22 July 2008

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. You can reach me at jblucks at berkeley dot edu.







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. It also paves the way for creative uses of the information, and the creation of better search interface tools.

For my PhD, I worked in the area of biophysics with David Nelson, where we used theoretical physics to study problems related to

  • 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

Education

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)

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