acd/labs onacd/labs on- · pdf file• nmr vs naming vs phys. chem. ... 11b nmr 13c nmr 15n...

ACD/Labs On LineACD/Labs On-Line Through theoug t e

Chemical Database Service

Dr. Don ParkinChemical Database ServiceDaresbury Laboratory

CSE Computational Science & Engineering Department1

y y

• Introduction/Background to CDS

• ACD/Labs at Daresbury

• Access

• Accounting

• User TrendsUser Trends• Web vs Client• NMR vs Naming vs Phys. Chem.


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Introduction• National Service started 1993 – central resource• Originally Grant funded by EPSRC but is now• Originally Grant funded by EPSRC but is now

a 3 Year contract with EPSRC• 2 Staff covered by contract• Provide networked access to up-to-date, high

quality comprehensive chemistry databases

• 2 Staff covered by contract

quality, comprehensive chemistry databases along with support and training

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• Service free of charge to usersfree

• Currently 3700+ users from 100+ sites

(UK Academics)


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Database coverageDatabase coverage

• Crystallography• Crystallography

• Organic Chemistry• Organic Chemistry

• Spectroscopy• Spectroscopy

• Physical Chemistry• Physical Chemistry


Spectroscopyp py• SpecInfo• From Chemical Concepts, containsFrom Chemical Concepts, contains

spectral data sets with their associated structure connection tables.

• A variety of features are available within the program to help with spectrum prediction and searching.

1H NMR

11B NMR

13C NMR

15N NMR

17O NMR

19F NMR

31P NMR

IR IR SPECTRA SPECTRA

MASS MASS SPECTRA SPECTRA

p p p g

130,000 10,238 359,000 7.661 5,184 32,780 25,656 20,898 138,727

193,000 186,000 8,800 15,400 26,100 ACD/Labs V11


Spectroscopy• SpecSurf - Web interface

p py


Physical Chemistryy y

produced byDETHERMproduced by

One of the world's largest thermophysical property databases of pure compounds andproperty databases of pure compounds and compound mixtures.

Contains ~6 Million data sets for around 134,000 systems (about 28,000 pure substances and 106 000 mixtures) coveringsubstances and 106,000 mixtures) covering nearly 500 properties.


Physical Chemistry

Data / Property Coverage

y yDETHERM

Data / Property Coverage


Physical ChemistryClient and Web access

y yDETHERM

Version 2.1

Client


Version 8 Trial July - October 2006There was an average of 80 users per month (over 200 unique users in total) making over 3,500 accesses and over 2,600 calculations (via I-lab).

Version 8 Trial July - October 2006

Users were from over 50 Institutes consisting of 80 departments, most of which were chemistry or related departments (e.g. chemical sciences).

5*, 5 and 4 graded chemistry departments accounted for almost three quarters of the users and accesses.

I-Lab ResultsAll elements of the databases were used with predictions being much higher than searching the databases ( 4:1)higher than searching the databases (~4:1).

62% of the usage was for the NMR data, of which 1H NMR was the highest, and pka predictions were just above solubility and logP


g , p p j y gpredictions.

Setup at DaresburyCDS Main

Server(Linux)Institute

p y

ProxyPass

log in using CDS ID and password

Firewall

cds11.dl.ac.uk

ACD/Labs Server(Windows

Institute Firewall cds.dl.ac.ukWindows

XP; Vista(Windows

Server 2003)DL Firewall

Institute USER MacFirewall

Mac

IE6, IE7, Firefox, Chrome, Safari etc.

CSE Computational Science & Engineering Department11LINUX

Access Problems

Vi CHEMSKETCHVia CHEMSKETCH

• Logging ongg g

• Proxy servers/Firewalls

• V11 vs V8

d illib dll• dmillib.dll


Access Problems

Some Universities such as Southampton could not

Logging on - Proxy servers/Firewalls

Some Universities such as Southampton could not log on at all using ChemSketch but had no problem with I-Lab.

The output from ChemSketch was being blocked by their firewall.

Network people at Southampton said it was probably due to poorly formed http protocol (possibilities included HTTP vs http)included HTTP vs http).

You could get around this by using a personal proxy server


– but not an ideal solution!

Access ProblemsVersion 8 vs Version 11

When we started using ChemSketch version 11, some users (including myself) had problems logging

O l i ll ld th l b f l

They all appear to have been successful logins from

on. Only occasionally would the logon be successful.

the point of view of the server. However, most were rejected by the Client with "Internal I-lab Error"

Replacing the dmillib.dll file in version 11 with the dmillib.dll file from version 8 solved this problem!


Accounting IssuesIn order to renew funding we need/like to know:-

g

• Who is logging in.

to know:

• How many times are they logging on (per month).

• Which access method are they using.y g(I-Lab or ChemSketch)

• What database they are accessing.y g

• Searching or Predicting.


• NMR vs Naming vs Physchem.

Accounting Issues

193.62.124.56 - cxxx [29/Jul/2008:09:18:20 +0000] GET /ilab/ HTTP/1.0 200 2880

gWeb logs (on cds.dl.ac.uk)

http://cds.dl.ac.uk/cds/ Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1; .NET CLR 1.1.4322)

59vig.dl.ac.uk - cyyy [29/Jul/2008:15:57:22 +0100] POST HTTP://cds.dl.ac.uk:80/ilab/perl/chsk.plHTTP/1.0 200 35923 - ChSkOnline/8.07 [en] (Win5.1; 2600; I; Nav)

IP address of user or machine name (e.g. 193.62.124.56)Name of user (-) User login ID (xxxx)[Date + relative to GMT]R t th d ( POST GET)Request method (e.g. POST, GET)URL relative to domain and HTTP protocol (e.g. /ilab/ HTTP/1.0)Status code: 200 – Successful

301 – Permanently redirected; 304 – Not Modified301 – Permanently redirected; 304 – Not Modified4xx – Client errors; 5xx – server errors

Size of the object returned to the client, in bytes (e.g. 35923 )URL the visitor came from (- is direct request)


User agent (software the visitor used to access this site – browser or ChemSketch)

Accounting IssuesChemSketch log files

g

Draw molecule then:-1. Log on2. Conduct a 13C NMR prediction3. Log out

xxxx [25/Jul/2008:09:43:01 POST HTTP://cds.dl.ac.uk:80/ilab/perl/chsk.pl HTTP/1.0 200 35923xxxx [25/Jul/2008:09:44:37 POST HTTP://cds.dl.ac.uk:80/ilab/perl/chsk.pl HTTP/1.0 200 543xxxx [25/Jul/2008:09:45:49 POST HTTP://cds.dl.ac.uk:80/ilab/perl/chsk.pl HTTP/1.0 200 43

Size of object

Found size of the object returned to the client was fairly consistent

Size of object29 443 4045 - 1,000 27

-> logout

fairly consistent. 1,000 - 10,000 8210,000 - 31,900 1035,921 - 35,923 8536,000 - 65,000 21

-> loginFor example for 1 month:-


36,000 65,000 21

[No indication of which database/calculation they performed]

Accounting IssuesgChemSketch log files

I-Lab Server

Main Server acd-test.cgi output.xxxx.UserIDacd test.cgi

d t l

/perl/chsk.plor

/chemsketch

input.xxxx.UserID

acdout.log


Accounting IssuesgChemSketch log files

ResultsResults

LCHSK - ict-nat-33-108.aston.ac.uk - ChSkOnline/11.00 [en] (Win5.1; 2600; I; Nav) - 18-09-08:17:55:27 - yyyyCHSK - HNMR - 18-09-08:17:58:18 - yyyy - <6secCHSK - HNMR - 18-09-08:18:12:40 - yyyy - <6secyyyyCHSK - HNMR - 18-09-08:18:13:28 - yyyy - <5secOCHSK - ict-nat-33-108.aston.ac.uk - ChSkOnline/11.00 [en] (Win5.1; 2600; I; Nav) - 18-09-08:18:13:55 - yyyyLCHSK - chpc-tl12.st-and.ac.uk - ChSkOnline/11.00 [en] (Win5.1; 2600; I; Nav) - 19-09-08:16:00:44 - zzzzCHSK - HNMRDB - 19-09-08:16:01:23 - zzzz - <6secCHSK HNMR 19 09 08:16:01:42 zzzz <5secCHSK - HNMR - 19-09-08:16:01:42 - zzzz - <5secOCHSK - chpc-tl12.st-and.ac.uk - ChSkOnline/11.00 [en] (Win5.1; 2600; I; Nav) - 19-09-08:16:10:56 - zzzzLCHSK - 152.71.172.99 - ChSkOnline/8.07 [en] (Win5.1; 2600; I; Nav) - 22-09-08:11:52:15 - vvvvCHSK - CNMR - 22-09-08:11:53:29 - vvvv - <9secCHSK - HNMR - 22-09-08:11:57:11 - vvvv - <7secOCHSK - 152.71.172.99 - ChSkOnline/8.07 [en] (Win5.1; 2600; I; Nav) - 22-09-08:11:59:52 – vvvvLCHSK - chpc-tl12.st-and.ac.uk - ChSkOnline/11.00 [en] (Win5.1; 2600; I; Nav) - 23-09-08:15:33:48 - zzzzCHSK - CNMR - 23-09-08:15:34:02 - zzzz - <18secOCHSK - chpc-tl12.st-and.ac.uk - ChSkOnline/11.00 [en] (Win5.1; 2600; I; Nav) - 23-09-08:15:38:51 - zzzz


Accounting IssuesI-Lab log files

g1. Log on; 2. Conduct a 13C NMR prediction; 3. Log out

[Removed entries for gif files etc ]

GET /ilab HTTP/1.1 301 302 http://cds.dl.ac.uk/cds/GET /ilab/ HTTP/1.1GET /ilab/ HTTP/1.1 200200 2880 http://cds.dl.ac.uk/cds/GET /ilab/info/menui.html HTTP/1.1 200 1575 http://cds.dl.ac.uk/ilab/GET /ilab/s1.css HTTP/1.1 200 1500 http://cds.dl.ac.uk/ilab/info/menui.htmlGET /ilab/perl/template pl?template=LOGIN INTRA HTTP/1 1 200 4683 http://cds dl ac uk/ilab/

[Removed entries for gif files etc.]

Login

GET /ilab/perl/template.pl?template=LOGIN_INTRA HTTP/1.1 200 4683 http://cds.dl.ac.uk/ilab/POST /ilab/perl/login3.pl HTTP/1.1 200 2735 http://cds.dl.ac.uk/ilab/perl/template.pl?template=LOGIN_INTRAPOST /ilab/perl/work.pl HTTP/1.1 200 16834 http://cds.dl.ac.uk/ilab/perl/login3.plGET /ilab/structure.html HTTP/1.1 200 5122 http://cds.dl.ac.uk/ilab/perl/work.plGET /ilab/cache.html HTTP/1.1 200 902 http://cds.dl.ac.uk/ilab/perl/work.plGET /ilab/perl/template.pl?template=INSTRUCTION HTTP/1.1 200 4880 http://cds.dl.ac.uk/ilab/perl/work.plGET /ilab/perl/template.pl?template=ILABLIST HTTP/1.1 200 8849 http://cds.dl.ac.uk/ilab/perl/work.pl

Enter I-Lab

p p p p p p pGET /ilab/applets/librinfo.dll HTTP/1.1 304 - -GET /ilab/structure.html HTTP/1.1 304 - http://cds.dl.ac.uk/ilab/perl/work.plGET /ilab/sda/sda.jar HTTP/1.1 304 - -GET /ilab/perl/template.pl?template=CNMR HTTP/1.1 200 8293 http://cds.dl.ac.uk/ilab/perl/work.plPOST /ilab/perl/calc.pl HTTP/1.1 200 5984 http://cds.dl.ac.uk/ilab/perl/template.pl?template=CNMRGET /ilab/perl/getFlag.pl?CALCULATE=CNMR&resFName=1........... HTTP/1.1 200 5979 http://cds.dl.ac.uk/ilab/perl/work.plGET /il b/ l/d l d l?CALCULATE CNMR& FN HTTP/1 1 200 5905 htt // d dl k/il b/ l/ k l

Calculate

GET /ilab/perl/downloadres.pl?CALCULATE=CNMR&resFName=…….… HTTP/1.1 200 5905 http://cds.dl.ac.uk/ilab/perl/work.plGET /ilab/perl/loadres.pl?CALCULATE=CNMR&resFName=……….s_name=CNMR HTTP/1.1 200 6138 http://cds.dl.ac.uk/ilab/perl/work.plGET /ilab/applets/ILSV.jar HTTP/1.1 304 - -GET /ilab/applets/images/ilsvtb.gif HTTP/1.1 304 - -GET /ilab/perl2/loadonce.pl?file=..\\tmp\\1221570000-00141609\\1221570000_316831221563802-9634.mol HTTP/1.1 200 910 -GET /ilab/perl2/loadonce.pl?file=1221570000_316831221563802-8337.NMR HTTP/1.1 200 44546 -GET /ilab/perl/logout.pl HTTP/1.1 302 - - Logout


GET /ilab/perl/logout.pl HTTP/1.1 302GET /ilab/perl/template.pl?template=LOGIN_INTRA HTTP/1.1 200 4683 http://cds.dl.ac.uk/ilab/

Logout


gLogin to I-Lab

GET /ilab/ HTTP/1.1PAIRS - EITHERGET /ilab HTTP/1.1 301 302GET /ilab/ HTTP/1.1 200GET /ilab/ HTTP/1.1 200 2880

GET /ilab/ HTTP/1.1zzzz [01/Apr/2008:23:43:42 301 302zzzz [01/Apr/2008:23:43:42 200 2880xxxx [02/Apr/2008:10:09:45 301 302xxxx [02/Apr/2008:10:09:45 200 2880

[02/A /2008 10 46 26 301 302 ORGET /ilab HTTP/1.1 301 302GET /ilab/ HTTP/1.1 304GET /ilab/ HTTP/1.1 304 -

vvvv [02/Apr/2008:10:46:26 301 302vvvv [02/Apr/2008:10:46:26 200 2880

xxxx [02/Apr/2008:10:57:15 301 302xxxx [02/Apr/2008:10:57:15 304 -

vvvv [02/Apr/2008:10:56:33 301 302

and get just single 200 or 304

Therefore count just 200or 304 status codes as

xxxx [02/Apr/2008:10:57:15 304 xxxx [02/Apr/2008:11:00:20 301 302xxxx [02/Apr/2008:11:00:20 304 -xxxx [02/Apr/2008:11:17:35 301 302xxxx [02/Apr/2008:11:17:35 304 -

[02/A /2008 15 54 19 301 302

and get just single 200 or 304

or 304 status codes as number of log ins?

xzxz [02/Apr/2008:15:54:19 301 302xzxz [02/Apr/2008:15:54:19 304 -

xzxz [02/Apr/2008:15:58:18 301 302xzxz [02/Apr/2008:15:58:18 304 - Also get just single 301

xzxz [02/Apr/2008:15:56:37 304 -


(301 – Permanently redirected; 304 – Not Modified)

[ paaaa [02/Apr/2008:16:56:33 200 2880

g j g


gLogin to I-Lab

Wh t b t l i 3 l k lWhat about login3.pl or work.pl

(When you press Enter I-Lab button )

A UAccesses UsersGET /ilab/ login3.pl work.pl GET /ilab/ login3.pl work.pl

April 146 121 173 35 32 32May 47 39 43 16 12 12June 83 76 85 30 26 26July 48 43 53 18 17 17August 80 72 79 23 20 20September 95 79 104 20 16 16


Press browser refresh button – get work.pl but not login3.pl

Accounting Issues

What database/calculation were they performing?I-Lab log files

g

When you choose from the drop down menus

GET /ilab/perl/template.pl?template=CNMR HTTP/1.1 200 8293 http://cds.dl.ac.uk/ilab/perl/work.pl

When you press the Calculate buttonOS / / / /1 1 200 98 // / / / ? CPOST /ilab/perl/calc.pl HTTP/1.1 200 5984 http://cds.dl.ac.uk/ilab/perl/template.pl?template=CNMR

GET /ilab/perl/getFlag.pl?CALCULATE=CNMR&resFName=1........... HTTP/1.1 200 5979http://cds.dl.ac.uk/ilab/perl/work.pl

GET /ilab/perl/downloadres pl?CALCULATE=CNMR&resFName= HTTP/1 1 200 5905GET /ilab/perl/downloadres.pl?CALCULATE CNMR&resFName …….… HTTP/1.1 200 5905http://cds.dl.ac.uk/ilab/perl/work.pl

GET /ilab/perl/loadres.pl?CALCULATE=CNMR&resFName=……….s_name=CNMR HTTP/1.1 200 6138http://cds.dl.ac.uk/ilab/perl/work.pl


calc.pl vs getFlag.pl vs downloadres.pl vs loadres.pl

Accounting ProblemsWhich file do you use?

I-Lab log filesg

template.pl calc.pl loadres.pl downloadres.pl getFlag.plADSBIO 1 1 1 1 1CNMR 15 9 15 15 9

CNMRDB 1 1 3 1 1HNMR 32 26 36 28 26

HNMRDB 26 25 56 24 24IUNAME 1 1 1 1 1LOGD 9 9 9 9 9LOGP 15 9 9 9 9

MOLVOLUM 1 1 1 1 1PARACHOR 1 1 1 1 1

PKA 3 2 2 2 2PKA 3 2 2 2 2SMILES 14 11 11 11 11SOLDB 2 2 8 6 2WSOL 13 12 19 19 12

TOTAL 134 110 172 128 109


TOTAL 134 110 172 128 109

ConclusionsClient vs Web

Users April May June July August Sept AverageUsers April May June July August Sept AverageI-LAB 35 15 30 18 23 20 24CHSK 16 11 17 12 12 24 15

Accesses April May June July August Sept Average

Unique Users 47 25 42 27 31 39 35

I-LAB 146 47 83 48 80 95 83CHSK 112 48 61 71 85 115 82TOTAL Accesses 258 95 144 119 165 210 165

Accesses per Users April May June July August Sept. Average

I-LAB 4.2 3.1 2.8 2.7 3.5 4.8 3.5


CHSK 7.0 4.4 3.6 5.9 7.1 4.8 5.5

Conclusions

April May June July Aug Sep Average

Calculations performed by Web UsersI-Lab

April May June July Aug Sep AverageAccesses 146 47 83 48 80 95 81

Login3.pl Users 32 12 26 17 20 16 21

Calc.pl Users 20 11 19 14 14 11 15

Calculations 256 110 198 88 132 122 151

Calculations per I-Lab Access 1.8 2.3 2.4 1.8 1.7 1.3 1.9

Calculations perCalc.pl User permonth

12.8 10.0 10.4 6.3 9.4 11.1 10


month

ConclusionsC l l i f d b Ch Sk h UCalculations performed by ChemSketch Users

I-Lab Av. 12/08-29/08 September 01/10-17/10Logins 81 38 115 111

Users 20 9 24 19Users 20 9 24 19

Calc. Users 16 8 20 14

C l l ti 198 136 198 168Calculations 198 136 198 168

Calculations per 2 3 5 1 7 1 5

Calculations perCalc. User/Month 9.8 17 9.9 12

Login 2 3.5 1.7 1.5


ConclusionsNMR vs Naming vs Physchem

DATABASE No. % No. %

NMR vs Naming vs Physchem. I-Lab ChemSketch (12/08/-17/10)

HNMR 131 17.5CNMR 79 10.5

HNMRDB 71 9.5CNMRDB 29 3.9

235 54.764 14.932 7.43 0.7

IUNAME 167 22.3SMILES 65 8.7

CASNAME 11 1.5

12 2.80 03 0.7

STRGEN 27 3.6PKA 88 11.7

WSOL 32 4.3LOGD 31 4 1

1 0.264 14.97 1.65 1 2LOGD 31 4.1

LOGP 18 2.4

Rest NMR 11 1.4

5 1.24 0.9

25 5.7


Rest PhysChem 22 2.8 3 0.7

ConclusionsNMR vs Naming vs Physchem. (I-Lab)

I-Lab ChemSketch (12/08/-15/10)NMR vs NAME vs PHYS.CHEM.

321 270 191

NMR vs NAME vs PHYS.CHEM.

325 16 75

41% 34.5% 24.5% 78% 4% 18%

PREDICTION DATABASE RATIO

NMR 220 106 2 : 1pKa+LogP

PREDICTION DATABASE RATIO

NMR 280 45 6 : 1pKa+LogPpKa+LogP

+Solubility 138 5 28 : 1

Total 358 111 3 : 1

pKa+LogP+Solubility 61 11 5.5 : 1

Total 358 111 6 : 1


Ch i l D t b S iChemical Database Service

CDSON-LINE

Thank you for your attention

ON LINE

Thank you for your attention….Dr. Don ParkinC i S i


Chemical Database ServiceDaresbury Laboratory

Introduction


Daresbury Laboratory, Warrington Cheshire

Help/supportp pp• Website: http://cds.dl.ac.uk

• About the Service: http://cds.dl.ac.uk/cds/service_info/about.html

U T i i d O li I f ti• User Training and Online Information:

o Manuals, Tutorials (e.g. ConQuest, Detherm and SpecSurf) and arranging Coursesand arranging Courses

o Flash movies

o CDS Newsletters

• Helpdesk available:

o E-mail [email protected] or Phone 01925 603162


acd/labs onacd/labs on- · pdf file• nmr vs naming vs phys. chem. ... 11b nmr 13c nmr 15n...

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