##master-page:HomepageTemplate
#format wiki
== Johan Hake, PhD ==
||<style="border: 0pt none ; text-align: left;">[[ImageLink(Johan_small.png, height=200)]]||<style="border: 0pt none ; vertical-align: top; text-align: left;">Department of Bioengineering[[BR]]University of California San Diego[[BR]]9500 Gilman Drive[[BR]]La Jolla, CA[[BR]]92093-0412[[BR]][[BR]]Email: [[MailTo(jhake AT SPAMFREE ucsd DOT edu)]][[BR]]Email: [[MailTo(johan.hake AT SPAMFREE gmail DOT com)]][[BR]] ||
Soon text about my history, scientific interests and achievements will appear here[[BR]]

=== Graphics ===
Selected graphics produced by me using inkscape [[BR]]
[[ImageLink(sarcomere_small.png,JohanHake/graphics, height=150)]]

=== Software ===
I am the main maintainer of several different software packages:
  * The Python interface of [https://launchpad.net/dolfin DOLFIN] a Finite element library within the umbrella of [http://www.fenicsproject.org FEniCS] (C++/Python).
  * [https://launchpad.net/gillstep GillStep] a tool to define and solve discrete and stochastic Markov models using a modified Gillespie solver (C++/Python)
  * [https://launchpad.net/subcell SubCell] a simulation tool for arbitrary reaction diffusion equation based on [http://www.fenicsproject.org FEniCS ] (Python)
  * GAMer a surface mesh improvement tool within the software library of [http://www.fetk.org FEtk], which can be integrated into [http://www.blender.org Blender] for a nice Gui user experience, [attachment:NBCR-techmseries-28.10.10.pdf see here]. It generates volumetric meshes using [http://tetgen.berlios.de tetgen]. [http://folk.uio.no/hake/fetk/gamer-snapshot.tar.gz download] (C/Python)
  

=== Talks ===
[attachment:nbcr-si2011-mesoscale-blamer.pdf Mesh improvements using] [http://www.blender.org Blender] and [http://www.fetk.org/codes/gamer GAMer][[BR]]
[attachment:nbcr-si2011-mesoscale-blamer-tutorial.pdf Mesh improvement tutorial using] [http://www.blender.org Blender] and [http://www.fetk.org/codes/gamer GAMer][[BR]]
[attachment:nbcr-si2011-mesoscale-subcell.pdf Talk on SubCell] a software solving general reaction-diffusion equations using [http://www.fenicsproject.org FEniCS] [[BR]]
[attachment:nbcr-si2011-mesoscale-subcell-tutorial.pdf Tutorial on SubCell] a software solving general reaction-diffusion equations using [http://www.fenicsproject.org FEniCS][[BR]]
[attachment:mesh_smoothening_using_gamer.pdf Mesh improvements using] [http://www.fetk.org/codes/gamer GAMer][[BR]]
[attachment:introduction_to_FEM_using_FEniCS.pdf Introduction to Finite element] method using [http://www.fenicsproject.org FEniCS] [[BR]]
[attachment:session-instructions.pdf SI2010 session instructions] [[BR]]
[attachment:NBCR-techmseries-28.10.10.pdf NBCR techseries 10/28/10] [[BR]]

----
 . CategoryHomepage