From ipanag at hydro.civil.ntua.gr Tue Sep 5 08:20:13 2006 From: ipanag at hydro.civil.ntua.gr (Iraklis Panagiotakis) Date: Tue Sep 5 10:52:43 2006 Subject: [Biothermokinetics] Kinetics of bacterial mixed cultures Message-ID: <1687.147.102.156.170.1157462413.squirrel@www.hydro.ntua.gr> Dear group, I have cultivated anaerobic mixed cultures and I am trying to test their ability to decompose some organic compounds under different environmental conditions. Currently I am trying to start studying the appropriate bibliography about bacterial kinetics in order to stimulate their behaviour. Is this possible for mixed cultures? Is there any basic reading for bacterial kinetics that I have to start with? Is there any basic reading of kinetic coefficients measurements in the lab? Should I try to find a software to model their kinetics? Any help would be valuable. Thank you. -- Iraklis Panagiotakis PhD candidate Department of Water Resources, Hydraulic & Maritime Engineering Faculty of Civil Engineering National Technical University of Athens Iroon Polytechneiou 5 157 80 Zografou tel. ++30 210 7721610 From atzus at gmx.de Tue Sep 5 15:05:16 2006 From: atzus at gmx.de (Atzus) Date: Tue Sep 5 15:40:26 2006 Subject: [Biothermokinetics] Kinetics of bacterial mixed cultures In-Reply-To: <1687.147.102.156.170.1157462413.squirrel@www.hydro.ntua.gr> References: <1687.147.102.156.170.1157462413.squirrel@www.hydro.ntua.gr> Message-ID: <44FDD87C.7030604@gmx.de> Hi all, hi Iraklis. > I have cultivated anaerobic mixed cultures and I am trying to test their > ability to decompose some organic compounds under different environmental > conditions. Currently I am trying to start studying the appropriate > bibliography about bacterial kinetics in order to stimulate their > behaviour. I am not sure what you mean by stimulate (or is this a nice typo, did you mean "simulate"?). > Is there any basic reading for bacterial kinetics that I have to start with? I would read the following books in this order: @BOOK{Cornish-Bowden2004, title = {Fundamentals of Enzyme Kinetics}, publisher = {Portland Press}, year = {2004}, author = {Athel Cornish-Bowden}, edition = {3.}, note = {ISBN: 1855781581} } @BOOK{Fell1996, title = {Understanding the Control of Metabolism}, publisher = {Ashgate Publishing}, year = {1996}, author = {David Fell}, note = {ISBN: 185578047X} } @BOOK{Heinrich1996, title = {The Regulation Of Cellular Systems}, publisher = {Springer}, year = {1996}, author = {Reinhart Heinrich and Stefan Schuster}, edition = {1.}, note = {ISBN: 0412032619} } > Is there any basic reading of kinetic coefficients measurements in the lab? In addition to the above-mentioned this may be a good resource if you are looking for coefficients: http://www.brenda.uni-koeln.de/ An additional recommended reading focusing on wet lab methods? Don't have one right now. > Should I try to find a software to model their kinetics? If you really want to try to build a kinetic model, I would suggest: http://www.copasi.org/ or http://sbw.sourceforge.net/ One warning: Before you start with the modeling process, I would rethink the approach. A kinetic model may not be what you are searching for. The modeling procedure should focus on the questions to be answered. What exactly do you want to achieve with the model? Kai From dalia.hassanin at hindawi.com Thu Sep 7 07:43:42 2006 From: dalia.hassanin at hindawi.com (Dalia Hassanin) Date: Thu Sep 7 08:33:45 2006 Subject: [Biothermokinetics] C4P for the new special issue of EURASIP Journal on Bioinformatics and Systems Biology Message-ID: <450013FE.9070101@hindawi.com> Information Theoretic Methods for Bioinformatics Call for Papers Information theoretic methods for modeling are at the center of the current efforts to interpret bioinformatics data. The high pace at which new technologies are developed for collecting genomic and proteomic data requires a sustained effort to provide powerful methods for modeling the data acquired. Recent advances in universal modeling and minimum description length techniques have been shown to be well suited for modeling and analyzing such data. This special issue calls for contributions to modeling of data arising in bioinformatics and systems biology by information theoretic means. Submissions should address theoretical developments, computational aspects, or specific applications. Suitable topics for this special issue include but are not limited to: Normalized maximum-likelihood (NML) universal models Minimum description length (MDL) techniques Microarray data modeling Denoising of genomic data Pattern recognition Data compression-based modeling Authors should follow the EURASIP JBSB manuscript format described at the journal site http://www.hindawi.com/GetJournal.aspx?journal=BSB. Prospective authors should submit an electronic copy of their complete manuscript through the EURASIP JBSB's Manuscript Tracking System at http://www.hindawi.com/mts/, according to the following timetable: Manuscript Due February 1, 2007 Acceptance Notification May 1, 2007 Final Manuscript Due July 1, 2007 Publication Date 3rd Quarter, 2007 Guest Editors: Jorma Rissanen, Computer Learning Research Center, University of London, Royal Holloway,TW20 0EX, UK Peter Gr?nwald, Centrum voor Wiskunde en Informatica (CWI), National Research Institute for Mathematics and Computer Science, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands Jukka Heikkonen, Laboratory of Computational Engineering, Helsinki University of Technology, P.O. Box 9203, 02015 HUT, Finland Petri Myllym?ki, Department of Computer Science, University of Helsinki, P.O. Box 68 (Gustaf H?llstr?min katu 2b), 00014, Finland Teemu Roos, Complex Systems Computation Group, Helsinki Institute for Information Technology, University of Helsinki, P.O.Box 68, 00014, Finland Juho Rousu, Department of Computer Science, University of Helsinki, P.O. Box 68 (Gustaf H?llstr?min katu 2b), 00014, Finland For more information please contact Dalia.hassanin@hindawi.com