User:Julius B. Lucks

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[[Image:JBL.jpg|150px|left|Julius B. Lucks]]
[[Image:JBL.jpg|150px|left|Julius B. Lucks]]
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I am a recent(!) PhD from Harvard, where I worked on problems in biophysics related to viruses with [http://www.physics.harvard.edu/people/facpages/nelson.html David Nelson].  During my PhD, I became interested in problems ranging from structural properties of viral capsids (and the underlying theory of geometrical defects in curved lattices that is required), to understanding phage genomics.
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I am a [http://millerinstitute.berkeley.edu/ Miller Fellow] at the University of California, Berkeley, in the lab of [http://genomics.lbl.gov/People.html Adam Arkin].  I am also the lead developer of the [http://export.arxiv.org/api_help arXiv.org API].
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In addition to the science and programming, I am a co-chair of the [[OpenWetWare:Steering_committee/Outreach_chairs|OWW Outreach Effort]] where we are coordinating local outreach officers to actively recruit new members to the OWW community. Interested in becoming a local outreach member? - [[OpenWetWare_talk:Steering_committee/Outreach_chairs|contact us!]]
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Currently, I am  at the [http://arxiv.org e-print arXiv] at Cornell with [http://en.wikipedia.org/wiki/Paul_Ginsparg Paul Ginsparg], where I will stay until I start a [http://millerinstitute.berkeley.edu/ Miller Fellowship] with [http://genomics.lbl.gov/People.html Adam Arkin] in January '08.
 
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In addition to reading up on potential post-doc projects, I am a co-chair of the [[OpenWetWare:Steering_committee/Outreach_chairs|OWW Outreach Effort]] where we are coordinating local outreach officers to actively recruit new members to the OWW community.  Interested in becoming a local outreach member? - [[OpenWetWare_talk:Steering_committee/Outreach_chairs|contact us!]]
 
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I also spent some time recently writing 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].
 
== Academics ==
== Academics ==
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== Interests ==
== Interests ==
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In addition to biophysics, 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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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.  To address this, a group of friends and I got together and made [http://maplit.hopto.org mapLit].  [http://maplit.hopto.org mapLit] is a new way to visualize literature search results that uses nested tree views for displaying related articles in context.  There are also convenience features that allow easy annotation of search results, saving of search results to work offline and share results, and the ability to connect saved searches online at a later date.  We appreciate any [mailto:maplit@gmail.com feedback on mapLit!]
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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!
*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]].
*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.
*Using the internet for fast publication of results.
**Broad community ranking of the usefulness/integrity of such results.
**Broad community ranking of the usefulness/integrity of such results.
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I hope to continue working on some of these ideas at the [http://arxiv.org arXiv].
 
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!
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!
== Tools I Like ==
== Tools I Like ==
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*Python
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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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**[http://www.linuxjournal.com/article/3882 Eric Raymond's thoughts] on Python vs. Perl
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*Perl
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**Perl-CGI - check out [http://slyjbl.hopto.org/PLD/ The Pica Literature Database]
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*[http://www.rubyonrails.org/ Ruby on Rails]
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**If you haven't seen the [http://www.rubyonrails.org/screencasts screencasts], they will blow your mind.
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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.
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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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>
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 has been on my list to learn for a while now - even more reason to do so.
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Lisp is awesome.
== Inspiration ==
== Inspiration ==
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*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 ===

Revision as of 15:57, 1 December 2007

Julius B. Lucks

I am a Miller Fellow at the University of California, Berkeley, in the lab of Adam Arkin. I am also the lead developer of the arXiv.org API.

In addition to the science and programming, I am a co-chair of the OWW Outreach Effort where we are coordinating local outreach officers to actively recruit new members to the OWW community. Interested in becoming a local outreach member? - contact us!



Academics

Check out my oww home page for more info on the projects I am working on.

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 You are Lisp.  Very few people like you (Probably because you use too many parenthesis (You better stop it (Reallly)))
Which Programming Language are You?
Lisp is awesome.

Inspiration

There are some really great thinkers out there ...

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

Publications

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)

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. B. Lucks, Y. Kafri. Dynamics of RNA Translocation through a Nanopore.

Arxiv: q-bio.BM/0703028 (FREE)

J. B. Lucks, D. R. Nelson, G. Kudla, J. B. Plotkin. Genome landscapes and bacteriophage codon usage.

Arxiv: arXiv:0708.2038v1 (q-bio.GN) (FREE)

Contact

My email address is lucks at fas dot harvard dot edu, or you can email me through OWW.

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