Monday, May 22, 2006

"maybe interesting paper" list

JCB Table of Contents: Jun 5, 2006; 173 (5)

Ups1p, a conserved intermembrane space protein, regulates mitochondrial shape and alternative topogenesis of Mgm1p
H. Sesaki, C.D. Dunn, M. Iijima, K.A. Shepard, M.P. Yaffe, C.E. Machamer, and R.E. Jensen

Microtubules can bear enhanced compressive loads in living cells because of lateral reinforcement
C.P. Brangwynne, F.C. MacKintosh, S. Kumar, N.A. Geisse, J. Talbot, L. Mahadevan, K.K. Parker, D.E. Ingber, and D.A. Weitz

Membrane lateral diffusion and capture of CFTR within transient confinement zones
Ian R Bates, Benedict Hebert, Yishan Luo, Jie Liao, Alexia I Bachir, David L Kolin, Paul W Wiseman, and John W Hanrahan
Biophys. J. published 19 May 2006, 10.1529/biophysj.106.084830

Current Opinion in Cell Biology
Volume 18, Issue 3, Pages 229-348 (June 2006)

The road much traveled: trafficking in the cell nucleus
Pages 284-290
Stanislaw A Gorski, Miroslav Dundr and Tom Misteli

DNA damage repair: anytime, anywhere?

Pages 240-246
Jeroen Essers, Wim Vermeulen and Adriaan B Houtsmuller

Thursday, May 11, 2006

coding: modified vecfield analyzer (IgorPro) VEC9_BiDirectionForce_Histo()

created a new function VEC9_BiDirectionForce_Histo()

prupose: the flow rate ratio has been calculated in "Away, Normal, Towards" directions (3 directional categories). The new version calculates in two different directions: away and towards. The largest difference in this calculation is that the vectorial component (projection of the vector to the axis that connects reference point and the origin of the vector: cosine of the relative angle) of the flow is determined and integrated in each direction. For example, if 10 proteins are moving with a velocity of 2^0.5 towards 45 degrees against the reference point, the flow it self would be 10 * 2^0.5 but the vectorial component towards the reference point is 10 * 2^0.5 * cosine(45).

created associated funcitons
V_CheckBinaryRoughDir() //060511

Cell Mechanics Seminar

I went yesterday to the Cell and Tissue Mechanics seminar @ BIOMS, Uni. Heidelberg, organized by Ulrich Schwarz.A great seminar, I would say. here is the PDF of Prof. Schwarz's lecture. Basics on hydrodynamics and viscoelasticity were explained in the seminar. In further series, there will be presentaiton on actual experiments and analysis. From the imaging side, the interpretation will be to extract strain and stress from displacements we observe under microscopes.

Tuesday, May 09, 2006

IgorPro Function K_averageCurves1D_toMax

Function K_averageCurves1D_toMax(listingwavename,resultAvewavename)

For averaging 1D curves with different data length.
-Generates average wave, sd wave,sem wave.
-Need to create a text wave containing a list of wave names.

** waves does not have to have a same number of rows. the averaged wave will be with
the maximum number of points, and errors will be calculated if there are at least 3 data are available.

Monday, May 08, 2006

CMCI seminar, FRAP lecture, Google Calender

Notes on CMCI seminar held last Friday is now available.

I would say::

- The award for the "Best Preparation" goes to Felipe. I think he made special measurements for his talk, with different parameters for the anisotropic diffusion filtering to clearly explain its power.

- Jerome's tracking program could be further extended with Graph-theory approach (cost & flow) such as the one by Danuser group to make it even more robust.

- I was very much attacted to Python scripting, which Peter presented.

- Julien showed simple but in-depth analysis using Kyomograph + Modelling. I guess his brain is filled with springs stretching and contracting.

- Francesco's talk was very informative, well explained principles on fluctuation analysis. I happend to know Michael (the guy who coded the 3D tracking program in IgorPro) in karate dojo, so I told him "Ok, you don't only do punching and kicking".

- Chaitanya told us about his challenges towards quantifying MT asters: measurement of radial shape could be probably connected to Thomas's presentation on Shape evaluation for angiogenesis.

- Thomas showed the real power of image processing: very sophisticated approach for measuring and extracting parameters out of the branching complex shape of vessels.

My talk? Don't forget "Dogs are dogs, cats are cats, and the Golgi is the Golgi"!


I made a lecture this morning, more details and basics on FRAP for the internal course organized by ALMF team. The talk was recorded by Luis, so people who wants to see it can watch it.


I made a public Google calender so those of you who are interested, please include "CMCI@EMBL" calender in yours.

Wednesday, May 03, 2006

Writing ImageJ Plug-In! A Beginner Course

For those of you who want to develop own plug-in for ImageJ to do custom image processing and analysis, but not knowing how to start out, there will be a start-up tutorial. There will be four times of weekly lectures given by the EMBL JAVA guru Cihan Cetin. Be aware, he will assign homeworks!

Cihan is now planning the dates. Please contact me if you are willing to participate.