[EuroPython] Trying to submit a talk, error

Mon May 2 00:01:56 CEST 2005

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: sjj698 at zepler.org

MSN Login (sjj698 at hotmail.com)
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