Re: [Biopredyn_pi] BioPreDyn: software integration (task 3.5) -- ACTIONS NEEDED --

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) 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 -- ------------------------------------------------------------- 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(a)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 -------------------------------------------------------------