Hi, Sorry to mail you, i guess you must get too many already. I am trying to submit a talk for europython (last min :-) and i cant get the webstite to work, i keep getting the same error. (error at the end of this email). Would it be possible to put forward my presentation proposal to you in an email? (here it is),
Many thanks Steven Title ------------------------------------------------------------------ Storage Resource Broker (SRB), Large scientific data and Python Abstract (max 200) ------------------------------------------------------------------ The BioSimGrid (www.biosimgrid.org) project is used with in the biochemical community to manage large amounts of simulation data. Each biochemical simulation produces trajectories which store the location and velocity of each atom in a protein over a given time period. Each trajectory can be 5-20GB in size and the BioSimGrid project can store over 2000 trajectories. We addresses these issues by delivering a distributed database system, to enable more effective storage, access and exchange of biomolecular simulation data, utilising Python as the integration language and flatfiles for storage. The flatfile distribution is managed using a Storage Resource Broker (SRB, http://www.sdsc.edu/srb/) and controlled via a limited python interface. To exploit the efficiency of the flatfiles for the trajectory data and the power of relational databases for the metadata, we present a hybrid approach to storing the data, using (i) SRB to manage flatfiles and using (ii) Oracle10g to store the metadata across 6 distributes sites. ------------------------------------------------------------------ Long description ------------------------------------------------------------------ Computer simulations play a vital role in biochemical research. By simulating the interactions of all atoms within a molecule or protein, the biochemical properties of the structure can be revealed. One important application of such Molecular Dynamics and Monte-Carlo simulations is predictive modelling in drug discovery, where the motion of proteins are important. These simulations are computationally demanding and they produce huge amount of data which is analysed by a variety of methods in order to obtain biochemical properties. Generally, these data are stored at the laboratory where they have been computed in a proprietary format which is unique to the simulation code that has been used. This constrains the sharing of data and results within the biochemistry community therefore the data can generally not be compared easily with post processing tools due to the varying data formats. This talk covers how the BioSimGrid project utilises python to produce a framework which stores the data as well as allows users to submit processing scripts to process the data. The data are structured into two key areas, the trajectory data and the metadata. As the metadata is small and relational, it is stored in a database, curently Oracle 10g. This database is replicated across our 6 sites and accessed using the Python interfaces. The trajectory data is 5-20GB and not very suited to a relational database, so for storage and processing requirements we have produced a framework which stores and retrieves the data into a Storage Resource Broker (SRB) using python. SRB enables us to deposit data at any site/location and have it available to all sites thus eliminating the need to transport or record the location of the data. There are currently many interfaces to SRB for other languages as well as a Windows based application and a very basic python interface. This talk will also look into the existing API as well as ongoing work, it will cover the advantages and disadvantages of SRB, providing a practical example showing how it can be used to store extremely large volumes of data. --------------------------------- -----------------------WEB PAGE ERROR------------------------------------- Web.Sync.srend.FormError: Either your session timed out, or you came here through an incomplete URL. Please start again. /home/caps/release/lib/python2.3/site-packages/twisted/internet/threads.py, line 37 in _putResultInDeferred 35 from twisted.internet import reactor 36 try: 37 result = f(*args, **kwargs) 38 except: Locals reactor twisted.internet.default.SelectReactor instance at 0x40539f8c <twisted.internet.default.SelectReactor instance at 0x40539f8c> f Function _call_method in file /home/caps/src/caps/Web/Sync/utils.py at line 12 kwargs Dictionary instance @ 0x40c47acc args (<Client.SynchronousClient.ClientServices object at 0x40bbc0cc>, {'report': <Client.SynchronousClient.ServiceBlm object at 0x40ba828c>, 'bookmarks': <Client.SynchronousClient.ServiceBlm object at 0x40ba8eec>, 'base': <Client.SynchronousClient.ServiceBlm object at 0x40ba8eac>, 'guirole': <Client.SynchronousClient.ServiceBlm object at 0x40bb996c>, 'CAPSconference': <Client.SynchronousClient.ServiceBlm object at 0x40bb9b0c>}, <bound method presentation._makePF of <presentation.presentation object at 0x40b87a4c>>, <nevow.context.PageContext object at 0x40d39fec>, None, None) /home/caps/src/caps/Web/Sync/utils.py, line 19 in _call_method 17 f_globals.update(blmdict) 18 19 return method(*args, **kwargs) 20 Locals blmdict Dictionary instance @ 0x40c5702creport <Client.SynchronousClient.ServiceBlm object at 0x40ba828c> bookmarks <Client.SynchronousClient.ServiceBlm object at 0x40ba8eec> base <Client.SynchronousClient.ServiceBlm object at 0x40ba8eac> guirole <Client.SynchronousClient.ServiceBlm object at 0x40bb996c> CAPSconference <Client.SynchronousClient.ServiceBlm object at 0x40bb9b0c> f_globals Dictionary instance @ 0x40c82cecSpeakers <class 'presentation.Speakers'> utils <module 'Web.Sync.utils' from '/home/caps/src/caps/Web/Sync/utils.pyc'> talkupdate <class 'presentation.talkupdate'> PresentationForm <class 'presentation.PresentationForm'> annotate <module 'formless.annotate' from '/home/caps/src/nevow-0.3/formless/annotate.pyc'> report <Client.SynchronousClient.ServiceBlm object at 0x40ba828c> DurationSorter <class 'presentation.DurationSorter'> EmailAddresses <class 'presentation.EmailAddresses'> bookmarks <Client.SynchronousClient.ServiceBlm object at 0x40ba8eec> TalkTitle <class 'presentation.TalkTitle'> getSession Function getSession in file ./presentation.py at line 14 conferenceData <class 'presentation.conferenceData'> srend <module 'Web.Sync.srend' from '/home/caps/src/caps/Web/Sync/srend.pyc'> ICurrentSpeaker <class 'presentation.ICurrentSpeaker'> SpeakerForm <class 'presentation.SpeakerForm'> IPresentationForm <class 'presentation.IPresentationForm'> configurable <module 'formless.configurable' from '/home/caps/src/nevow-0.3/formless/configurable.pyc'> formutils <module 'formless.formutils' from '/home/caps/src/nevow-0.3/formless/formutils.pyc'> guirole <Client.SynchronousClient.ServiceBlm object at 0x40bb996c> EmailAddress <class 'register.EmailAddress'> presentation <class 'presentation.presentation'> email <module 'email' from '/home/caps/release/lib/python2.3/email/__init__.pyc'> CAPSconference <Client.SynchronousClient.ServiceBlm object at 0x40bb9b0c> IPresentation <class 'presentation.IPresentation'> ITalkupdateForm <class 'presentation.ITalkupdateForm'> tags <module 'nevow.tags' from '/home/caps/src/nevow-0.3/nevow/tags.pyc'> builtin dictionary Dictionary instance @ 0x401c868chelp site._Helper instance at 0x401f056c Type help() for interactive help, or help(object) for help about object. vars <built-in function vars> SyntaxError <class exceptions.SyntaxError at 0x401ca7dc> unicode <type 'unicode'> UnicodeDecodeError <class exceptions.UnicodeDecodeError at 0x401cad1c> isinstance <built-in function isinstance> copyright site._Printer instance at 0x401f070c Copyright (c) 2001, 2002, 2003 Python Software Foundation. All Rights Reserved. Copyright (c) 2000 BeOpen.com. All Rights Reserved. Copyright (c) 1995-2001 Corporation for National Research Initiatives. All Rights Reserved. Copyright (c) 1991-1995 Stichting Mathematisch Centrum, Amsterdam. All Rights Reserved. NameError <class exceptions.NameError at 0x401ca6bc> dict <type 'dict'> input <built-in function input> oct <built-in function oct> SystemExit <class exceptions.SystemExit at 0x401ca38c> StandardError <class exceptions.StandardError at 0x401ca32c> repr <built-in function repr> IndexError <class exceptions.IndexError at 0x401ca95c> False False RuntimeWarning <class exceptions.RuntimeWarning at 0x401df05c> list <type 'list'> iter <built-in function iter> reload <built-in function reload> Warning <class exceptions.Warning at 0x401cae9c> round <built-in function round> dir <built-in function dir> cmp <built-in function cmp> reduce <built-in function reduce> intern <built-in function intern> issubclass <built-in function issubclass> Ellipsis Ellipsis hash <built-in function hash> locals <built-in function locals> slice <type 'slice'> FloatingPointError <class exceptions.FloatingPointError at 0x401cab0c> sum <built-in function sum> OverflowWarning <class exceptions.OverflowWarning at 0x401df02c> getattr <built-in function getattr> abs <built-in function abs> exit Use Ctrl-D (i.e. EOF) to exit. True True FutureWarning <class exceptions.FutureWarning at 0x401df08c> None None EOFError <class exceptions.EOFError at 0x401ca59c> len <built-in function len> credits site._Printer instance at 0x401f06ec Thanks to CWI, CNRI, BeOpen.com, Zope Corporation and a cast of thousands for supporting Python development. See www.python.org for more information. __name__ __builtin__ ord <built-in function ord> super <type 'super'> TypeError <class exceptions.TypeError at 0x401ca35c> license site._Printer instance at 0x401f066c Type license() to see the full license text KeyboardInterrupt <class exceptions.KeyboardInterrupt at 0x401ca3ec> UserWarning <class exceptions.UserWarning at 0x401caecc> filter <built-in function filter> range <built-in function range> staticmethod <type 'staticmethod'> SystemError <class exceptions.SystemError at 0x401cae3c> pow <built-in function pow> RuntimeError <class exceptions.RuntimeError at 0x401ca5cc> float <type 'float'> StopIteration <class exceptions.StopIteration at 0x401ca2fc> globals <built-in function globals> divmod <built-in function divmod> enumerate <type 'enumerate'> apply <built-in function apply> LookupError <class exceptions.LookupError at 0x401ca92c> open <type 'file'> quit Use Ctrl-D (i.e. EOF) to exit. basestring <type 'basestring'> UnicodeError <class exceptions.UnicodeError at 0x401cabcc> zip <built-in function zip> hex <built-in function hex> long <type 'long'> ReferenceError <class exceptions.ReferenceError at 0x401cae0c> ImportError <class exceptions.ImportError at 0x401ca44c> chr <built-in function chr> __import__ <built-in function __import__> type <type 'type'> __doc__ Built-in functions, exceptions, and other objects. Noteworthy: None is the `nil' object; Ellipsis represents `...' in slices. Exception <class exceptions.Exception at 0x401ca2cc> tuple <type 'tuple'> UnicodeTranslateError <class exceptions.UnicodeTranslateError at 0x401cadac> UnicodeEncodeError <class exceptions.UnicodeEncodeError at 0x401cac5c> IOError <class exceptions.IOError at 0x401ca4dc> hasattr <built-in function hasattr> delattr <built-in function delattr> setattr <built-in function setattr> raw_input <built-in function raw_input> SyntaxWarning <class exceptions.SyntaxWarning at 0x401cafbc> compile <built-in function compile> ArithmeticError <class exceptions.ArithmeticError at 0x401ca9ec> str <type 'str'> property <type 'property'> MemoryError <class exceptions.MemoryError at 0x401cae6c> int <type 'int'> xrange <type 'xrange'> KeyError <class exceptions.KeyError at 0x401ca9bc> coerce <built-in function coerce> PendingDeprecationWarning <class exceptions.PendingDeprecationWarning at 0x401caf8c> file <type 'file'> EnvironmentError <class exceptions.EnvironmentError at 0x401ca47c> unichr <built-in function unichr> id <built-in function id> OSError <class exceptions.OSError at 0x401ca53c> DeprecationWarning <class exceptions.DeprecationWarning at 0x401caf2c> min <built-in function min> execfile <built-in function execfile> complex <type 'complex'> bool <type 'bool'> ValueError <class exceptions.ValueError at 0x401cab6c> NotImplemented NotImplemented map <built-in function map> buffer <type 'buffer'> max <built-in function max> object <type 'object'> TabError <class exceptions.TabError at 0x401ca89c> callable <built-in function callable> ZeroDivisionError <class exceptions.ZeroDivisionError at 0x401caa7c> eval <built-in function eval> __debug__ True IndentationError <class exceptions.IndentationError at 0x401ca86c> AssertionError <class exceptions.AssertionError at 0x401ca8fc> classmethod <type 'classmethod'> UnboundLocalError <class exceptions.UnboundLocalError at 0x401ca71c> NotImplementedError <class exceptions.NotImplementedError at 0x401ca62c> AttributeError <class exceptions.AttributeError at 0x401ca7ac> OverflowError <class exceptions.OverflowError at 0x401caa1c> __file__ ./presentation.py EmailAddressesRenderer <class presentation.EmailAddressesRenderer at 0x40d42e3c> base <Client.SynchronousClient.ServiceBlm object at 0x40ba8eac> __doc__ None webform <module 'formless.webform' from '/home/caps/src/nevow-0.3/formless/webform.pyc'> services <Client.SynchronousClient.ClientServices object at 0x40bbc0cc> __name__ presentation compy <module 'nevow.compy' from '/home/caps/src/nevow-0.3/nevow/compy.pyc'> iformless <module 'formless.iformless' from '/home/caps/src/nevow-0.3/formless/iformless.pyc'> types <module 'types' from '/home/caps/release/lib/python2.3/types.pyc'> inevow <module 'nevow.inevow' from '/home/caps/src/nevow-0.3/nevow/inevow.pyc'> IListTalks <class 'presentation.IListTalks'> listtalks <class 'presentation.listtalks'> TalkupdateForm <class 'presentation.TalkupdateForm'> server http://pbf.strakt.com:8080/ itertools <module 'itertools' from '/home/caps/release/lib/python2.3/lib-dynload/itertools.so'> ISpeakersForm <class 'presentation.ISpeakersForm'> components <module 'twisted.python.components' from '/home/caps/release/lib/python2.3/site-packages/twisted/python/components.pyc'> kwargs Dictionary instance @ 0x40a5acec args (<nevow.context.PageContext object at 0x40d39fec>, None, None) method Method _makePF in file ./presentation.py at line 474 ./presentation.py, line 496 in _makePF 494 form.speakers = [s.emailAddress[0] for s in p.speakers] 495 else: 496 form.conference = self._getconference(context)[0] 497 form.track = self._gettrack(context)[0] Locals context <nevow.context.PageContext object at 0x40d39fec> form <presentation.PresentationForm object at 0x40a4d58c> self <presentation.presentation object at 0x40b87a4c> ./presentation.py, line 546 in _getconference 544 pass 545 546 raise srend.FormError('Either your session timed out, or you came here through an incomplete URL. Please start again.') 547 Globals srend <module 'Web.Sync.srend' from '/home/caps/src/caps/Web/Sync/srend.pyc'> Web.Sync.srend.FormError: Either your session timed out, or you came here through an incomplete URL. Please start again. -- ------------------------------------------------- Steven Johnston (MEng) Computational Engineering and Design Research Group School of Engineering Science University of Southampton Highfield Southampton SO17 1BJ Telephone: + 44 (0) 23 8059 8348 Mob phone: + 44 (0) 77 6439 1901 Email: [EMAIL PROTECTED] MSN Login ([EMAIL PROTECTED]) --------------------------------------------------- _______________________________________________ EuroPython mailing list [email protected] http://mail.python.org/mailman/listinfo/europython
