David Nickerson wrote: >> I am working on developing a CellML model (using external code) of >> transcriptional control in yeast which is 23 MB in size. I hope to >> eventually do a similar thing for organisms which have much more >> complicated sets of interactions, in which case this size may grow >> substantially. >> > > so you have 23MB of XML? Cool! Even combining all my models I have less > than 7MB, and even then I'm sure that figure includes some simulation > results. > My model is entirely generated from experimental data, none of it is written by hand (aside from a one-page script used to generate CellML from the relational database). > I guess an interesting test would be uploading it to the model > repository to see how that handles such a large model (presuming you > have a CellML 1.0 model). > It is currently a CellML 1.0 model. I'm not sure I want to break the live Plone, however. I'm not sure it is much use to anyone else at this stage, however. > >> If anyone on this list is interested in similar problems (I presume >> similar issues come up in a range of systems biology problems, whether >> you are working with CellML or SBML), I would welcome your feedback and >> suggestions, and perhaps we could collaborate . >> > > I really have no idea what an transcriptional control in yeast model > looks like, but my initial thought would be to abstract out any similar > math and import common declarations - I'm guessing you have already done > this if its possible. > My model only has machine-learning external-code in it, it doesn't have any equations at the moment. Just to give you an idea of what it looks like...
<model xmlns="http://www.cellml.org/cellml/1.0#"; name="interactions"> <component name="PAU8"> <variable name="sig_PAU8" initial_value="0" units="signal_level" public_interface="out"/> <variable name="sig_SUT1" units="signal_level" public_interface="in"/> <variable name="sig_STE12" units="signal_level" public_interface="in"/> <variable name="sig_ADR1" units="signal_level" public_interface="in"/> <variable name="sig_YAP5" units="signal_level" public_interface="in"/> <variable name="sig_RME1" units="signal_level" public_interface="in"/> <variable name="sig_TEC1" units="signal_level" public_interface="in"/> <variable name="sig_SWI5" units="signal_level" public_interface="in"/> <variable name="sig_ARR1" units="signal_level" public_interface="in"/> <variable name="sig_MET31" units="signal_level" public_interface="in"/> <variable name="sig_RLM1" units="signal_level" public_interface="in"/> <variable name="sig_INO4" units="signal_level" public_interface="in"/> <variable name="sig_RAP1" units="signal_level" public_interface="in"/> <variable name="sig_MOT3" units="signal_level" public_interface="in"/> <math xmlns="http://www.w3.org/1998/Math/MathML";> <apply><eq/> <ci>sig_PAU8</ci> <apply> <csymbol definitionURL="http://www.bioeng.auckland.ac.nz/people/miller/black_box/k-nearest-neighbours";>blackbox</csymbol> <ci>sig_SUT1</ci> <ci>sig_STE12</ci> <ci>sig_ADR1</ci> <ci>sig_YAP5</ci> <ci>sig_RME1</ci> <ci>sig_TEC1</ci> <ci>sig_SWI5</ci> <ci>sig_ARR1</ci> <ci>sig_MET31</ci> <ci>sig_RLM1</ci> <ci>sig_INO4</ci> <ci>sig_RAP1</ci> <ci>sig_MOT3</ci> </apply> </apply> </math> </component> <component name="YAL067W_A"> <variable name="sig_YAL067W_A" initial_value="0" units="signal_level" public_interface="out"/> <variable name="sig_SPT23" units="signal_level" public_interface="in"/> <variable name="sig_STE12" units="signal_level" public_interface="in"/> <variable name="sig_DAL80" units="signal_level" public_interface="in"/> <variable name="sig_YAP5" units="signal_level" public_interface="in"/> <variable name="sig_BAS1" units="signal_level" public_interface="in"/> <variable name="sig_DIG1" units="signal_level" public_interface="in"/> <variable name="sig_PHO2" units="signal_level" public_interface="in"/> <variable name="sig_HAP2" units="signal_level" public_interface="in"/> <variable name="sig_PHD1" units="signal_level" public_interface="in"/> <variable name="sig_GLN3" units="signal_level" public_interface="in"/> <math xmlns="http://www.w3.org/1998/Math/MathML";> <apply><eq/> <ci>sig_YAL067W_A</ci> <apply> <csymbol definitionURL="http://www.bioeng.auckland.ac.nz/people/miller/black_box/k-nearest-neighbours";>blackbox</csymbol> <ci>sig_SPT23</ci> <ci>sig_STE12</ci> <ci>sig_DAL80</ci> <ci>sig_YAP5</ci> <ci>sig_BAS1</ci> <ci>sig_DIG1</ci> <ci>sig_PHO2</ci> <ci>sig_HAP2</ci> <ci>sig_PHD1</ci> <ci>sig_GLN3</ci> </apply> </apply> </math> </component> ... Note that the initial_value="0" is a place-holder, I could abstract out my blackbox function calls based on the number of parameters (it is variable, from 1 through to 41, in this case, although there is no theoretical limit on how many putative transcription factors could affect a signal). However, I suspect that this would not solve the performance problems (it takes 8 seconds to load the model into the CellML API, but this would be much costlier if it had to load literally thousands of copies of the same file. This could be optimised using a cache, but I still don't think it will help very much). > >> This creates some unique issues for CellML processing tools: >> 1) Just parsing the CellML model (especially with a DOM-type parser >> which stores all the nodes into a tree, but probably with any type of >> parser) is very slow. >> > > it might be interesting to look at doing some simple task to check the > performance of DOM vs SAX based tools? I have found in the past that > with 500MB "fieldML" files that the SAX parser used in CMGUI was quite > fast at parsing the file - especially if you go from a gzip compressed file. > Possibly, but the current CellML API implementation needs an underlying DOM representation, and while 8s to parse the file is a long time, it is probably one of the smaller issues compared to the time to actually do things with the model. > >> 2) The CellML model might not all fit in memory at the same time, >> especially if the model gets to be multi-gigabyte. It might be possible >> to make use of swap to deal with this, but if the algorithms don't have >> explicit control over when things are swapped in and out, it will be >> hard to work with such a model. >> > > I think if you have a model getting that large then there needs to be > some serious thinking about how to handle such models...but generally > can't you just let the OS worry about swapping in and out as required? > Or would you expect a customised scheme for a particular application to > be more efficient? > It probably depends on the algorithm. However, if you have a huge amount of data, you might be better to build some sort of index, and to do this efficiently, it is generally better to keep the amount of data in memory low enough to avoid swapping, and explicitly manage this based on knowledge of when the data will be accessed, rather than inferences based on when the data was accessed historically. A relational database could probably give us this for free (but the exact requirements would depend on the algorithm using the API). > >> C) Another leaner API, read-only CellML API (perhaps based off the same >> IDLs, but with certain functionality, like the ability to modify the >> model, or set mutation event listeners, unavailable). We could add a >> SAX-style event dispatcher instead, to allow users to save any >> information they do want from extension elements, which will also not be >> kept in the model. Comments, white-space, and so on would all be >> stripped unlike in the current CellML API implementation. Tools which >> are currently using the full CellML API but only require read-only >> access (e.g. the CCGS) might be able to just 'flick the switch' and >> benefit from the leaner API. >> > > This would probably be beneficial even for those of us without such > large models - especially if it is as easy as flicking a switch to swap > between the complete and restricted implementations. > This is probably true, although I have got the time complexity reasonable by using a memoisation scheme, so it is really the memory utilisation that is the biggest problem. Best regards, Andrew _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
