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<  Membrane Packing Algorithms Archive  ~  The Vesicle Builder [jar]

PostPosted: 06.03.2012, 11:03
User avatarSite AdminPosts: 199Joined: 20.03.2006, 15:01
The Vesicle Builder

This is the first version of our Vesicle Builder. It was first presented at the VizBi2012:

http://vizbi.org/Posters/2012/C17

You can just download it as a jar and use it in conjunction with the MembraneEditor. The import process is easy, just look here:

http://www.cellmicrocosmos.org/index_cm ... 000_import

The source code will be available after publication.

Please let me know if you find any bugs or if you have proposals for its improvement. There is already a number of improvements we will be working on in the future. For example, the strong feature of the MembraneEditor to mark microdomains is not supported by this algorithm at the moment. Heterogeneity is - of course - supported, as well as multiple layers. The algorithm is partly based on the Random Placing Algorithm which is Standard in the MembraneEditor.

CmME features not supported yet:
  • Microdomains
  • Protein Placing Extension (automatic placing of proteins with PDB_TM and OPM)
  • Average Area per Lipid Computation in MembraneEditor GUI (from version 1.11, the plugin internally provides an APL approximation)


Manuel's Simulation Analysis Scripts
If you did a simulation with GROMACS of a vesicle generated with this plugin which you would like to analyze, please have a look at Manuel's sub forum:
viewtopic.php?f=18&t=762&p=1572


Authors: Beatrice Giuliari, Yan Zhou, Tim Dingersen, Björn Sommer
Beta Tester: Manuel Krüger

:shock:Version 1.11pre The Triple One Release (PRE/Beta Test Version)
  • Pre Beta Release: 18.12.2014
  • differentiation between EC and IC values
  • fixed termination bug (did not terminate at some point)
  • added 3 different termination modes
    • proposed lipid number: as internally proposed by the Vesicle Builder
    • custom lipid number: the user can define values for EC and IC
    • no termination: runs until stopped
  • improved micelle handling
  • improved Scheduler
  • updated scheduler from Random Placing v. 1.10
  • added option buttons from Random Placing v. 1.10
  • improved schedule if only a single option is selected, corrected mistake in this context in Random Placing v. 1.10
    -> Random Placing v. 1.11 (part of the MembraneEditor) and Vesicle Builder v. 1.11 use now the same scheduler
  • GUI update
    • added PRO and ROOKIE Gui mode toggle
    • there is also a variable to change the default GUI mode
    • added a checkbox to toggle the extended protocol for the lipid type APL
  • the new version computes the area per lipid (APL) and number for each lipid type
    • for the target values
    • for the effective values (if algorithm is finished)
  • extended protocol
  • improved computation of initial size of vesicle
  • tried to fix Vector bug for large vesicles by updating the variable abValues_IC simultaneously to abValues_EC, I am still not sure if this is a Java bug or a bug of the algorithm
Attachment:
File comment: The Vesicle Builder 1.11pre

compatible to MembraneEditor version >= Cm2.2.2
VesicleBuilder.jar [31.32 KiB]
Downloaded 1109 times




Version 1.10 Beatrice's Master Thesis Version
  • Alpha Release 03.07.2014
  • supports now also micelle building (activate fill only EC)
  • improved automatic packing
  • version compatible to the actual version >= Cm2.2.2
Attachment:
File comment: The Vesicle Builder 1.10

compatible to MembraneEditor version >= Cm2.2.2
VesicleBuilder.jar [38.97 KiB]
Downloaded 1173 times




Authors: Beatrice Giuliari, Yan Zhou, Tim Dingersen, Björn Sommer

Version 1.09 !NEW Release for Cm2.2.2!
  • Alpha Release 21.01.2014
  • Makes use of the new Membrane Packing Algorithm Interface function: this.getJ3DBranchGroup() by providing a preview function for the size of the vesicle
  • drastically improved packing capabilities added by Beatrice Giuliari in context of her master thesis topic:
    • the area per lipid computation is improved, leading to a better approximation of the initial number of lipids to place (this applies especially to heterogeneous membranes, also with larger size differences, e.g. with Cardiolipin and Cholesterol), and
    • a simple annealing process similar to the one from the Random Placing Algorithm is now integrated
    • :arrow: the lipid density was drastically increased in comparison to the previous VecicleBuilder versions
  • version compatible to the actual version >= Cm2.2.2
Attachment:
File comment: The Vesicle Builder 1.09

compatible to MembraneEditor version >= Cm2.2.2
VesicleBuilder.jar [20.15 KiB]
Downloaded 1130 times




Authors: Yan Zhou, Tim Dingersen, Björn Sommer

Version 1.02
  • Alpha Release 21.09.2013
  • version compatible to the actual version >= Cm2.2.1_2
Attachment:
File comment: The Vesicle Builder 1.02

compatible to MembraneEditor version >= Cm2.2.1_2
VesicleBuilder.jar [24.03 KiB]
Downloaded 1173 times



Version 1.01
  • Alpha Release 30.04.2012
  • improved definition of the three semi-axes: they match now the X/Y/Z-axes of the MembraneView
  • average area per lipid is computed in relation to the desired lipid number and the sizes of the semi-axes
Attachment:
File comment: The Vesicle Builder 1.01

compatible to MembraneEditor version <= Cm2.2.1_1
VesicleBuilder.jar [12.48 KiB]
Downloaded 1217 times



Version 1.0
  • VizBi 2012 Alpha Release
Attachment:
File comment: The Vesicle Builder 1.0

compatible to MembraneEditor version <= Cm2.2.1_1
VesicleBuilder.jar [13.22 KiB]
Downloaded 1239 times



Offline Profile ICQ
PostPosted: 04.10.2018, 09:57
Posts: 11Joined: 03.10.2018, 11:28
thank you friend for sharing this post on the vesicle builder and also about the help essays. This first version of our Vesicle Builder seem worth getting indeed, certainly a good and helpful post this is.


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