From owner-chemistry@ccl.net Thu Jun 28 07:31:01 2012
From: "Sidney Ramos Santana santanasidney{}yahoo.com.br" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Free Sparse Matrix-Matrix Multiplication Library ?
Message-Id: <-47151-120628035928-9467-duMIk8V+4xYqEwBYy4cXyA . server.ccl.net>
X-Original-From: "Sidney Ramos Santana" <santanasidney(~)yahoo.com.br>
Date: Thu, 28 Jun 2012 03:59:27 -0400


Sent to CCL by: "Sidney Ramos Santana" [santanasidney__yahoo.com.br]
Dear CCL Subscribers,

Due the different time zones,

good day, good afternoon, or, good night.

I am looking for a Free Sparse Matrix-Matrix 

Multiplication Library (written in C/C++ or Fortran) 

that can be implemented into a SCF procedure.

Does anyone know anything about this ?

If yes, please could you send me any information

about that.

Thank you for any help you can provide.

Best regards.

Sidney R. Santana
santanasidney_at_yahoo.com.br


From owner-chemistry@ccl.net Thu Jun 28 08:06:01 2012
From: "Pablo Englebienne p.englebienne a tue.nl" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Lipid membrane modeling tool
Message-Id: <-47152-120628052808-21791-oP42rbygZO+bgjQ1bIlZ/A#,#server.ccl.net>
X-Original-From: Pablo Englebienne <p.englebienne|,|tue.nl>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 28 Jun 2012 11:27:59 +0200
MIME-Version: 1.0


Sent to CCL by: Pablo Englebienne [p.englebienne : tue.nl]
Hi Felipe, I'm not sure specifically what you are trying to accomplish 
with respect to the lipid membranes, but if what you're looking after is 
atomistic MD simulations involving a lipid bilayer and perhaps some 
solutes, Gromacs may be able to handle it.

I found the tutorials written by Justin Lemkul quite instructive as a 
starting point: 
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

Tutorial #2 deals specifically with building a lipid membrane with a 
peptide solute.

Regards,
Pablo

Pablo Englebienne, PhD
Dept. of Biomedical Engineering, group Computational Biology
Dept. of Chemistry and Chemical Engineering
Institute for Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

On 05/20/2012 03:37 PM, Felipe Pineda pideca^-^hotmail.com wrote:
> Sent to CCL by: "Felipe  Pineda" [pideca:+:hotmail.com]
> Dear CCLers!
>
> I'd greatly appreciate any pointer to state-of-the-art, non-commercial molecular modeling tools for mono- and bilayer lipid membranes. I searched the CCL archive, but couldn't find any useful information.
>
> Many thanks in advance,
>
> Felipe
> Computational Chemistry and Biochemistry Lab
> Linnaeus University
> Kalmar, Sweden>
>


From owner-chemistry@ccl.net Thu Jun 28 12:11:00 2012
From: "Jim Kress ccl_nospam . kressworks.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Free Sparse Matrix-Matrix Multiplication Library ?
Message-Id: <-47153-120628083123-26134-WRm2YYiWJMwmphgBQh3pkQ%a%server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam^kressworks.com>
Content-Language: en-us
Content-Transfer-Encoding: 7bit
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	charset="us-ascii"
Date: Thu, 28 Jun 2012 08:31:05 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]


The Internet is your friend:

http://www.ask.com/web?l=dis&o=10148&qsrc=2873&q=Free%20Sparse%20Matrix-Matr
ix%20Multiplication%20Library

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com_-_ccl.net
> [mailto:owner-chemistry+ccl_nospam==kressworks.com_-_ccl.net] On Behalf
> Of Sidney Ramos Santana santanasidney{}yahoo.com.br
> Sent: Thursday, June 28, 2012 3:59 AM
> To: Kress, Jim 
> Subject: CCL: Free Sparse Matrix-Matrix Multiplication Library ?
> 
> 
> Sent to CCL by: "Sidney Ramos Santana" [santanasidney__yahoo.com.br]
> Dear CCL Subscribers,
> 
> Due the different time zones,
> 
> good day, good afternoon, or, good night.
> 
> I am looking for a Free Sparse Matrix-Matrix
> 
> Multiplication Library (written in C/C++ or Fortran)
> 
> that can be implemented into a SCF procedure.
> 
> Does anyone know anything about this ?
> 
> If yes, please could you send me any information
> 
> about that.
> 
> Thank you for any help you can provide.
> 
> Best regards.
> 
> Sidney R. Santana
> santanasidney_at_yahoo.com.brTo
> recover the email address of the author of the message, please change the
> strange characters on the top line to the _-_ sign. You can also look up the
X-
> Original-From: line in the mail header.>


From owner-chemistry@ccl.net Thu Jun 28 12:46:00 2012
From: "Alex Allardyce aallardyce^chemaxon.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Program announcement: ChemAxon US UGM, Sept 25-26, Wellesley, MA
Message-Id: <-47154-120628102531-27619-p57myq/Tri41XiyWvdlh7A++server.ccl.net>
X-Original-From: Alex Allardyce <aallardyce^chemaxon.com>
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	boundary="----=_Part_1334_20223467.1340893520859"
Date: Thu, 28 Jun 2012 16:25:19 +0200 (CEST)
MIME-Version: 1.0


Sent to CCL by: Alex Allardyce [aallardyce[A]chemaxon.com]
------=_Part_1334_20223467.1340893520859
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable


Excuse cross postings.=20

We are announcing the program and calling for participants for ChemAxon's 5=
th US User Group Meeting (US-UGM) which will take place on September 25-26t=
h in Wellesley, MA. For the satellite One to One and One to Many topic sess=
ions (Sept 24th) and Training (Sept 27th) sessions see details below=20

Highlights of the event:=20

    * Program is launched with presentations from industry users including;=
 Boehringer Ingelheim, BMS, Broad Inst, Eli Lilly, GSK, NIH, Novartis, Pear=
son, Takeda and Wiley. Full presentation titles below.=20
    * Program: http://www.chemaxon.com/events/ugm-boston-2012/#program=20
    * The UGM is followed by a training day (Sept 27th) with two different =
tracks: one for developers and the other for end users.=20
    * Prior to the UGM, on the afternoon of Sept 24th, we host an afternoon=
 of One to One meetings for users and 2 focused One to Many sessions for Bi=
ologics Registration and SharePoint.=20
    * Well regarded on and off site socials for networking and to keep the =
ideas moving.=20

I hope you can join us for what, I think, is our best program yet.=20

BR=20
Alex=20

Useful links:=20
Program: http://www.chemaxon.com/events/ugm-boston-2012/#program=20
More information: http://www.chemaxon.com/events/ugm-boston-2012/#overview=
=20
Registration: http://www.chemaxon.com/events/ugm-boston-2012-registration/=
=20
One to One & One to Many Sessions: http://www.chemaxon.com/events/ugm-bosto=
n-2012/#onetomany=20
Developer Training: http://www.chemaxon.com/events/ugm-boston-2012/#develop=
er=20
End user training details: http://www.chemaxon.com/events/ugm-boston-2012/#=
appfocus=20
UGM archives - slides and video and meeting reports from Wendy Warr and Yvo=
nne Martin: http://www.chemaxon.com/ugm-archive/=20

Program: User Presentation titles and Institutions=20

01 Chemistry Infrastructure Migration in Global Pharmaceutical Company: Con=
cerns and Reality. Zhenbin (Benjamin) Li, Boehringer Ingelheim=20
02 Patent Analytics for Drug Discovery via Instant JChem. Dana Vanderwall, =
Bristol-Myers Squibb=20
03 Keynote: Future-proofing - managing systems in rapidly changing times. R=
amesh Durvasula & Alex Drijver, Bristol-Myers Squibb & ChemAxon=20
04 Development of a Stereochemical Structure-Activity Relationships Viewer =
to Analyze HTS Data Generated from DOS Compound Collections. Carol Mulroone=
y, Broad Institute=20
05 Assisted Data Exploration in Chemical Biology. Dennis Moccia, Cognative =
Data Works=20
06 The Lilly Open Innovation Drug Discovery Program. Daniel Robertson, Eli =
Lilly=20
07 Registration as a service: The full story after half-year. Rama Bhamidip=
ati & Akos Papp, GSK & ChemAxon=20
08 Advances in text mining for chemical information: an update on the ChiKE=
L project. David Milward, Daniel Bonniot, Linguamatics & ChemAxon=20
09 Cloudy with a touch of Cheminformatics. Rajarshi Guha, NIH - NCGI=20
10 Migrating away from ISIS with ChemAxon's help. Debra Kassabian, Novartis=
=20
11 An approach to developing a Compound Registration system using JChem Bas=
e and JChem Cartridge. Bob Trucchi, Nuova Stella=20
12 Pearson Education and ChemAxon: Partnership to develop educational Marvi=
nSketch. Jeanne Zalesky, Pearson Education=20
13 GPCR Informatics: Structure/Properties and Pharmacological Correlations.=
 Danni Harris, RTI International=20
14 Compound Progression Workflow Process. Matthew Pustelnik, Takeda Califor=
nia=20
15 Just Another Chemical Query (ChemQ) Tool or Not. Matthew Pustelnik, Take=
da California=20
16 Compounds for indications, indications for compounds. John Irwin, UCSF=
=20
17 Enhancing the User Experience for Wiley Chemistry Content. Neil Pearson,=
 Wiley=20




Alex Allardyce=20
Marketing Dir.=20
ChemAxon Ltd=20
Z=C3=A1hony u. 7. Building HX, Budapest, 1031 Hungary=20
http://www.chemaxon.com=20
Tel: +361 453 0435=20
Fax: +361 4532659=20




------=_Part_1334_20223467.1340893520859
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<html><head><style type=3D'text/css'>p { margin: 0; }</style></head><body><=
div style=3D'font-family: arial,helvetica,sans-serif; font-size: 10pt; colo=
r: #000000'><style>p { margin: 0; }</style><div style=3D"font-family: arial=
,helvetica,sans-serif; font-size: 10pt; color: rgb(0, 0, 0);">Excuse cross =
postings.<br><br>We are announcing the program and calling for participants=
 for ChemAxon's 5th US User Group Meeting (US-UGM) which will take place on=
 September 25-26th in Wellesley, MA. For the satellite One to One and One t=
o Many topic sessions (Sept 24th) and Training (Sept 27th) sessions see det=
ails below<br><br>Highlights of the event:<br><ul><li>Program is launched w=
ith presentations from industry users including;=20
Boehringer Ingelheim, BMS, Broad Inst, Eli Lilly, GSK, NIH, Novartis,=20
Pearson, Takeda and Wiley. Full presentation titles below. <br></li><li>Pro=
gram: http://www.chemaxon.com/events/ugm-boston-2012/#program</li><li>The U=
GM is followed by a training day (Sept 27th) with two different tracks: one=
 for developers and the other for end users.</li><li>Prior to the UGM, on t=
he afternoon of Sept 24th, we host an afternoon of One to One meetings for =
users and 2 focused One to Many sessions for Biologics Registration and Sha=
rePoint.&nbsp; </li><li>Well regarded on and off site socials for networkin=
g and to keep the ideas moving.</li></ul>I hope you can join us for what, I=
 think, is our best program yet.<br><br>BR<br>Alex<br><br>Useful links:<br>=
Program: http://www.chemaxon.com/events/ugm-boston-2012/#program<br>More in=
formation: http://www.chemaxon.com/events/ugm-boston-2012/#overview<br>Regi=
stration: http://www.chemaxon.com/events/ugm-boston-2012-registration/<br>O=
ne to One &amp; One to Many Sessions: http://www.chemaxon.com/events/ugm-bo=
ston-2012/#onetomany<br>Developer Training: http://www.chemaxon.com/events/=
ugm-boston-2012/#developer<br>End user training details: http://www.chemaxo=
n.com/events/ugm-boston-2012/#appfocus<br>UGM archives - slides and video a=
nd meeting reports from Wendy Warr and Yvonne Martin: http://www.chemaxon.c=
om/ugm-archive/<br><br>Program: User Presentation titles and Institutions<b=
r><br>01&nbsp;&nbsp;&nbsp; Chemistry Infrastructure Migration in Global Pha=
rmaceutical Company: Concerns and Reality.&nbsp;&nbsp;&nbsp; Zhenbin (Benja=
min) Li, Boehringer Ingelheim<br>02&nbsp;&nbsp;&nbsp; Patent Analytics for =
Drug Discovery via Instant JChem.&nbsp;&nbsp;&nbsp; Dana Vanderwall, Bristo=
l-Myers Squibb<br>03&nbsp;&nbsp;&nbsp; Keynote: Future-proofing - managing =
systems in rapidly changing times.&nbsp;&nbsp;&nbsp; Ramesh Durvasula &amp;=
 Alex Drijver, Bristol-Myers Squibb &amp; ChemAxon<br>04&nbsp;&nbsp;&nbsp; =
Development of a Stereochemical Structure-Activity Relationships Viewer to =
Analyze HTS Data Generated from DOS Compound Collections.&nbsp;&nbsp;&nbsp;=
 Carol Mulrooney, Broad Institute<br>05&nbsp;&nbsp;&nbsp; Assisted Data Exp=
loration in Chemical Biology.&nbsp;&nbsp;&nbsp; Dennis Moccia, Cognative Da=
ta Works<br>06&nbsp;&nbsp;&nbsp; The Lilly Open Innovation Drug Discovery P=
rogram.&nbsp;&nbsp;&nbsp; Daniel Robertson, Eli Lilly<br>07&nbsp;&nbsp;&nbs=
p; Registration as a service: The full story after half-year.&nbsp;&nbsp;&n=
bsp; Rama Bhamidipati &amp; Akos Papp, GSK &amp; ChemAxon<br>08&nbsp;&nbsp;=
&nbsp; Advances in text mining for chemical information: an update on the C=
hiKEL project.&nbsp;&nbsp;&nbsp; David Milward, Daniel Bonniot, Linguamatic=
s &amp; ChemAxon<br>09&nbsp;&nbsp;&nbsp; Cloudy with a touch of Cheminforma=
tics.&nbsp;&nbsp;&nbsp; Rajarshi Guha, NIH - NCGI<br>10&nbsp;&nbsp;&nbsp; M=
igrating away from ISIS with ChemAxon's help.&nbsp;&nbsp;&nbsp; Debra Kassa=
bian, Novartis<br>11&nbsp;&nbsp;&nbsp; An approach to developing a Compound=
 Registration system using JChem Base and JChem Cartridge.&nbsp;&nbsp;&nbsp=
; Bob Trucchi, Nuova Stella<br>12&nbsp;&nbsp;&nbsp; Pearson Education and C=
hemAxon: Partnership to develop educational MarvinSketch.&nbsp;&nbsp;&nbsp;=
 Jeanne Zalesky, Pearson Education<br>13&nbsp;&nbsp;&nbsp; GPCR Informatics=
: Structure/Properties and Pharmacological Correlations.&nbsp;&nbsp;&nbsp; =
Danni Harris, RTI International<br>14&nbsp;&nbsp;&nbsp; Compound Progressio=
n Workflow Process.&nbsp;&nbsp;&nbsp; Matthew Pustelnik, Takeda California<=
br>15&nbsp;&nbsp;&nbsp; Just Another Chemical Query (ChemQ) Tool or Not.&nb=
sp;&nbsp;&nbsp; Matthew Pustelnik, Takeda California<br>16&nbsp;&nbsp;&nbsp=
; Compounds for indications, indications for compounds.&nbsp;&nbsp;&nbsp; J=
ohn Irwin, UCSF<br>17&nbsp;&nbsp;&nbsp; Enhancing the User Experience for W=
iley Chemistry Content.&nbsp;&nbsp;&nbsp; Neil Pearson, Wiley<br><br><br><b=
r><br>Alex Allardyce<br>Marketing Dir.<br>ChemAxon Ltd<br>Z=C3=A1hony u. 7.=
 Building HX, Budapest, 1031 Hungary<br>http://www.chemaxon.com<br>Tel: +36=
1 453 0435<br>Fax: +361 4532659<br><br><div><span></span><br></div></div></=
div></body></html>
------=_Part_1334_20223467.1340893520859--


From owner-chemistry@ccl.net Thu Jun 28 14:29:00 2012
From: "Billy McCann bwm0005%x%tigermail.auburn.edu" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Free Sparse Matrix-Matrix Multiplication Library ?
Message-Id: <-47155-120628135422-30359-m8lXXb/GjNTeJzAkirBL3w{:}server.ccl.net>
X-Original-From: Billy McCann <bwm0005(!)tigermail.auburn.edu>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 28 Jun 2012 17:54:08 +0000
MIME-Version: 1.0


Sent to CCL by: Billy McCann [bwm0005#tigermail.auburn.edu]
http://math.nist.gov/spblas/

+++++++++++++++++++++++++
Billy Wayne McCann
Ph.D. Candidate
Orlando Acevedo Reseach
Auburn University, Alabama
Office # = 334.844.6948 
bwayne on irc.freenode.net
+++++++++++++++++++++++++


-----Original Message-----
> From: owner-chemistry+bwm0005==auburn.edu^ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu^ccl.net] On Behalf Of Jim Kress ccl_nospam . kressworks.com
Sent: Thursday, June 28, 2012 7:31 AM
To: Billy McCann
Subject: CCL: Free Sparse Matrix-Matrix Multiplication Library ?


Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]


The Internet is your friend:

http://www.ask.com/web?l=dis&o=10148&qsrc=2873&q=Free%20Sparse%20Matrix-Matr
ix%20Multiplication%20Library

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com[#]ccl.net
> [mailto:owner-chemistry+ccl_nospam==kressworks.com[#]ccl.net] On Behalf
> Of Sidney Ramos Santana santanasidney{}yahoo.com.br
> Sent: Thursday, June 28, 2012 3:59 AM
> To: Kress, Jim 
> Subject: CCL: Free Sparse Matrix-Matrix Multiplication Library ?
> 
> 
> Sent to CCL by: "Sidney Ramos Santana" [santanasidney__yahoo.com.br]
> Dear CCL Subscribers,
> 
> Due the different time zones,
> 
> good day, good afternoon, or, good night.
> 
> I am looking for a Free Sparse Matrix-Matrix
> 
> Multiplication Library (written in C/C++ or Fortran)
> 
> that can be implemented into a SCF procedure.
> 
> Does anyone know anything about this ?
> 
> If yes, please could you send me any information
> 
> about that.
> 
> Thank you for any help you can provide.
> 
> Best regards.
> 
> Sidney R. Santana
> santanasidney_at_yahoo.com.brTo
> recover the email address of the author of the message, please change the
> strange characters on the top line to the [#] sign. You can also look up the
X-
> Original-From: line in the mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt