<br><br><div class="gmail_quote">On Mon, Jun 29, 2009 at 11:11 PM, Marlon Pierce <span dir="ltr"><<a href="mailto:mpierce@cs.indiana.edu">mpierce@cs.indiana.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
* Taking a look at this now. I grabbed and built Jumbo 5.5-b1 from
SourceForge. "mvn clean install" fails some tests (I'm getting "JNI
InChI has failed to load the native libraries required"), but "mvn
clean install -Dmaven.test.skip=true" works (compiles).</div></blockquote><div><br>InChI is a menace because it's written in C and messy. JNIchi is a wrapper.<br><br>Does it run as well as compile?<br> <br></div>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div bgcolor="#ffffff" text="#000000"><br>
<br>
<br>
* Assuming my Jumbo version and build are OK, I need to generate CML
from PubChem with Jumbo. First, which Pubchem XML should I use? I
presume 3D version.<br>
</div></blockquote><div><br>You need jumbo converter. Then you should run PubChem2CML.<br><br>We need some modest docco here because I tend to run it from Eclipse. Nick has a clojure pipeline. I will talk with him tomorrow. If we can't work that I will create the docco.<br>
<br>P.<br><br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div bgcolor="#ffffff" text="#000000"><br>
<br>
* Finally, what is the command for doing this with Jumbo?<br>
<br>
<br>
Thanks, more questions to follow. <br><div><div></div><div class="h5">
<br>
<br>
Marlon<br>
<br>
<br>
Peter Murray-Rust wrote:
<blockquote type="cite">Great,<br>
hope we can set up some telcons anyway<br>
<br>
<div class="gmail_quote">On Fri, Jun 12, 2009 at 7:24 PM, Marlon
Pierce <span dir="ltr"><<a href="mailto:mpierce@cs.indiana.edu" target="_blank">mpierce@cs.indiana.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
My time over the next couple of weeks will be dominated by TeraGrid 09
preparation, but I will make some headway in getting started and will
be working in earnest by end of June.<br>
<font color="#888888"><br>
<br>
Marlon</font>
<div>
<div><br>
<br>
<br>
Peter Murray-Rust wrote:
<blockquote type="cite">Great - that's exciting Bill and I am sure
that it will be
invaluable for assignment. However I am focusssing on what we can
integrate today. The integration problems are not trivial and the more
that the components - or the sites - are modularised the faster
progress we shall<br>
<br>
It's important to be pragmatic at this stage - there are things we can
do now and things that are research. We should do both but we must make
sure that the infrastructure continues in a straight line. I detailed
what we could do at present (some as rough proof of concept) that could
fit into a linear workflow. We must make sure that the research efforts
in the pipeline I indicated are small as the integration of itself will
still be challenging. <br>
<br>
So I am propopsing that we should ask:<br>
* what can we do by Friday 19?<br>
* what can we do by the start of August?<br>
* what can we do in the rest of the project.<br>
<br>
Each part depends on the previous one:<br>
* Mark needs a few papers from Lee/Prasenjit which have good PDF
chemistry<br>
* PMR needs a few molecules and spectra in SVG<br>
* Marlon needs a few CML molecules and the NMREye workflow.<br>
<br>
I agree that Mark's work on general PDF parsing is exciting but we need
a stream of molecules for the later stages.<br>
<br>
I am also going to suggest that we try to arrange weekly telcons to
review progress. The problem of a pipeline/workflow is that all bits
have to be delivering.<br>
<br>
P.<br>
<br>
<br>
<br>
<div class="gmail_quote">On Fri, Jun 12, 2009 at 3:47 PM, WILLIAM
J
BROUWER <span dir="ltr"><<a href="mailto:wjb19@psu.edu" target="_blank">wjb19@psu.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>cool peter...<br>
<br>
I would also add that there's some mileage in
substructure & similarity search on spectra. Han gave a great talk
this
morning, there is strong application of his graph mining work to
building up
complicated spectra on the basis of simpler (sub)spectra...<br>
<br>
-bill <br>
<div>
<div><br>
<br>
On Fri, Jun 12, 2009 10:31 AM, <b>Peter Murray-Rust
<<a href="mailto:pm286@cam.ac.uk" target="_blank">pm286@cam.ac.uk</a>></b> wrote:<br>
<blockquote style="border-left: 1px solid rgb(0, 0, 0); padding-left: 3px; padding-right: 0px; margin-left: 3px; margin-right: 0px;">
<p>This is to review the subprojects
that the computational geeks in OREChem have put together over the last
few
days. (a) is long term, (b) is immediate<br>
(a) The general goal is to compute
NMR spectra for all new published compounds and compare them with
spectra. This
is a new approach "robot refereeing of chemistry publications" and any
differences suggest errors or new chemistry. This is long term (months)
and
consists of the following (as we have put on the wiki):<br>
* PSU-Lee/Prasenjit retrieve chemistry-rich docs from publisher sites
(ask for
forgiveness policy) and segment the papers into text+non-text (tables,
diagrams). This passes to:<br>
* Mark - Soton extracts molecules and spectra out
of this and converts them to SVG. The short-term goal is to get this
working by
the end of next week in a pragmatic form. (we do not mind if recall is
poor as
long as we get a few SVGs as we need to develop the machine-learning
and/or
heuristics and find out what unknown horrors we have to deal with. <br>
Bitmaps are rejected at this stage<br>
* PMR- cambridge develops heuristics to
interpret (i) molecules (ii) spectra (C13 and H1). These might later be
crowdsourced. The output is CML molecules and spectra. It is unlikely
we have
assignments<br>
* PSU - Bill+Karl. Analyse spectra with peak-fitting. <br>
* IU - Marlon.
(independently) molecules are passed to IU in CML and put into the
NMREye
workflow for computing peaks (below). IU run this automatically and
return
results in CML<br>
<br>
(b) To get IU up to speed we shall start immediately on
simple molecules from Pubchem. This involves just Cambridge and IU.<br>
* The
NMREye workflow has been developed and tested and should work on simple
organic
compounds. It consists of the following:<br>
- convert PubchemXML2CML (already available in JUMBO)<br>
-
convert CML to Gaussian input. We have an XSLT script, but could
convert this
to Java in an hour.<br>
- in parallel - create RDF metadata for
provenance to this point (as this does not survive the Gaussian run)<br>
... submit and run job ... (IU) ... and collect results<br>
-
convert LOG file to CML (JUMBOMarker, effectively done)<br>
- convert CML
to RDF (JUMBO). Add GaussianOWL dictionary in RDF<br>
<br>
upload RDFs into
reopository/tripleStore<br>
<br>
In (b) we would expect to get 10,000 - 100,000
small molecules from Pubchem of up to, say , 15 first row atoms. These
already
have 3D coordinates (I am ignoring conformers at this stage). The
process
should be automatic. Jobs take from 0.1 seconds to 1 day (probably) as
they
scale with N^4.<br>
<br>
P.<br>
<br>
I will try to send this to the Wiki<br>
<br clear="all">
<br>
-- <br>
Peter Murray-Rust<br>
Reader in Molecular
Informatics<br>
Unilever Centre, Dep. Of Chemistry<br>
University of
Cambridge<br>
CB2 1EW,
UK<br>
+44-1223-763069<br>
</p>
</blockquote>
<br>
<br>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Peter Murray-Rust<br>
Reader in Molecular Informatics<br>
Unilever Centre, Dep. Of Chemistry<br>
University of Cambridge<br>
CB2 1EW, UK<br>
+44-1223-763069<br>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Peter Murray-Rust<br>
Reader in Molecular Informatics<br>
Unilever Centre, Dep. Of Chemistry<br>
University of Cambridge<br>
CB2 1EW, UK<br>
+44-1223-763069<br>
</blockquote>
</div></div></div>
</blockquote></div><br><br clear="all"><br>-- <br>Peter Murray-Rust<br>Reader in Molecular Informatics<br>Unilever Centre, Dep. Of Chemistry<br>University of Cambridge<br>CB2 1EW, UK<br>+44-1223-763069<br>