Dear BioPreDyn PIs,
(cc Bertrand Moreau, CSM)
as you know, one of the key expected outcomes of BioPreDyn is:
"To deliver an integrated suite of tools and newly
developed/improved algorithms to support the entire
model building cycle."
This integrated suite will be done in the framework of WP3,
and, more in particular, software integration is the focus
of task 3.5 and deliverable D3.4.
Although this task is leaded by CWI, in close cooperation
with CSM, we are all (except FS) involved since we are all
expected to contribute with novel and existing algorithms.
During the writing of the proposal, and also during other
contacts afterwards, we basically agreed that CSM will receive
methods from the other partners and will re-implement them
in their integrated software framework.
The purpose of this email is to open a discussion on the
detailed road map to achieve this.
Following the proposal and the DIP of WP3 (attached again),
these are the key topics and actions needed (marked with
>>):
- CWI will develop an SB-cycle protocol with inputs from
all participants. >>Joke(CWI): could you please write a
draft
of this and distribute it so everyone can give feedback asap?
- Each partner should detail, in agreement with the
project proposal, their contributions (methods/tools),
including the expected date when this will be sent to
CSM and some technical details (purpose, language, I/O
formats, etc.) >> Eric/Bertrand(CSM): could you give
us a template of the minimum info you need for this?
Also, could you give us an example of an existing
software package using your framework? (if there is one)
>> ALL: please send the info on your planned contributions
following CSM's template
Finally, a suggestion: in the proposal (see also the DIP of WP3),
we also mentioned that INSIL will integrate some of these
algorithms into their own software framework. This enhances
the dissemination of the methods, a key objective of the
project. Maybe a subset of the methods can also be
integrated in COPASI. Feedback from Pedro on this?
What do the rest of you think about it?
Best regards,
Julio
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Prof. Julio R. Banga
BioProcess Engineering Group
Instituto de Investigaciones Marinas
(C.S.I.C.)
Spanish Council for Scientific Research
C/Eduardo Cabello 6
36208 Vigo (SPAIN)
E-mail: julio@iim.csic.es
Web http://www.iim.csic.es/~julio/
http://www.iim.csic.es/~gingproc/
Blog http://jrbanga.posterous.com/
Positions http://www.iim.csic.es/~julio/positions.html
ph: +34 986 214 473 (direct)
fax: +34 986 292 762
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