ASSIGNMENT 0

67 views
Skip to first unread message

Vinod Scaria

unread,
Jun 22, 2010, 12:01:17 AM6/22/10
to osdd-c...@googlegroups.com
Dear All,

I understand that many of you have been able to install and run CDK
successfully.
I would urge all who have successfully finished the assignment help
others , so that they can also keep upto the mark.

I would request you to add your queries and responses to the CDK sheet
shared with you
http://docs.google.com/document/edit?id=1hdXvQ4VENeKiqGVCnVkPku8t8brNzLtRZSO43iqy8nc&hl=en

I would also invite you to organise yourself into groups and specify
which sub-area you plan to work on (see example)
http://spreadsheets.google.com/ccc?key=0AkKaURo7T-SGdDNsR2RDYXE4dGRNcWtESEtNSnNPUGc&hl=en

Best regards
Vinod


--
----------------------------------------------------------
Dr Vinod Scaria
Scientist
G N Ramachandran Knowledge Centre for Genome Informatics,
Institute of Genomics and Integrative Biology (CSIR),
Mall Road, Delhi 110 007, India
E-mail: vin...@igib.res.in
Web: http://vinodscaria.rnabiology.org/
Mob: +91 9650466002

Lab Address: IGIB Extension Center at Naraina,
A93-94 Naraina Inds Area, Phase 1,Naraina, New Delhi -110 028, Ph-
+91-11-25895615, 45073677/88/99 | Fax no: +91-11-2766 7471
---------------------------------------------------------
What's New? Visit http://miracle.igib.res.in

NOTE
'This message, including any attachments, may contain confidential and
privileged information for the sole use of the intended recipient(s).
Review, use, distribution or disclosure by others is prohibited. If
you receive this message in error, please notify the sender by reply
e-mail and delete the message from all computers. Please note that
e-mails are susceptible to change. The sender will not accept
liability for the improper or incomplete transmission of the
information contained in this message.'

Amit Kumar Singh

unread,
Jun 22, 2010, 4:13:29 AM6/22/10
to osdd-c...@googlegroups.com
Sir I am unable to include my name and email ID and my sub-area in the master spreadsheet
 
http://spreadsheets.google.com/ccc?key=0AkKaURo7T-SGdDNsR2RDYXE4dGRNcWtESEtNSnNPUGc&hl=en#gid=0

my name is: Amit Kumar Singh

email id: amitbio123@gmail

sub area: cheminformatics


ramesh kumar

unread,
Jun 22, 2010, 6:36:44 AM6/22/10
to osdd-c...@googlegroups.com
sir, i want to know how to get a input and output file for CDK


--
You received this message because you are subscribed to the Google
Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
To post to this group, send email to osdd-c...@googlegroups.com
To unsubscribe from this group, send email to
osdd-cheminf...@googlegroups.com

Suma Avasthi

unread,
Jun 23, 2010, 3:02:50 AM6/23/10
to osdd-c...@googlegroups.com
unable to include my name too in the spreadsheets sir
T.Suma Avasthi
chemiinformatics
sumaa...@gmail.com


--
You received this message because you are subscribed to the Google
Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
To post to this group, send email to osdd-c...@googlegroups.com
To unsubscribe from this group, send email to
osdd-cheminf...@googlegroups.com



--
T.Suma
Project Associate
c/o Dr.Sharmistha Banerjee
Asst. Prof., Department of Biochemistry
&
c/o Dr.Niyaz Ahmed
Reader, Department of Biotechnology,
School of Life Sciences,
University of Hyderabad,
INDIA

jagmohan sharma

unread,
Jun 23, 2010, 5:33:07 AM6/23/10
to osdd-c...@googlegroups.com
how to include subfield.....
$*jagmohan sharma*$

vinod kumar

unread,
Jun 23, 2010, 5:53:53 AM6/23/10
to OSDD Cheminformatics
hi sharma
first you have to download sdf file of the compound from database. eg
pubchem and zinc
then downloaded file browse as input file to the cdk descriptor tool
ok
at a same time empty note pad text file browse out put file finally
run cdk descriptor.
after run output file will be open in excel...
if have doubt send a msg

from
vinod kumar hs
osdd

On Jun 23, 2:33 pm, jagmohan sharma <jagmohansharman...@gmail.com>
wrote:
> how to include subfield.....
>
> On Wed, Jun 23, 2010 at 12:32 PM, Suma Avasthi <sumaavas...@gmail.com>wrote:
>
>
>
> > unable to include my name too in the spreadsheets sir
> > *T.Suma Avasthi
> > chemiinformatics
> > sumaavas...@gmail.com*
>
> > On 22 June 2010 13:43, Amit Kumar Singh <amitbio...@gmail.com> wrote:
>
> >> Sir I am unable to include my name and email ID and my sub-area in the
> >> master spreadsheet
>
> >>http://spreadsheets.google.com/ccc?key=0AkKaURo7T-SGdDNsR2RDYXE4dGRNc...
>
> >> my name is: Amit Kumar Singh
>
> >> email id: amitbio123@gmail
>
> >> sub area: cheminformatics
>
> >>  --
> >> You received this message because you are subscribed to the Google
> >> Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> >> To post to this group, send email to osdd-c...@googlegroups.com
> >> To unsubscribe from this group, send email to
> >> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsu...@googlegroups.com>
>
> > --
> > T.Suma
> > Project Associate
> > c/o Dr.Sharmistha Banerjee
> > Asst. Prof., Department of Biochemistry
> > &
> > c/o Dr.Niyaz Ahmed
> > Reader, Department of Biotechnology,
> > School of Life Sciences,
> > University of Hyderabad,
> > INDIA
>
> >  --
> > You received this message because you are subscribed to the Google
> > Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> > To post to this group, send email to osdd-c...@googlegroups.com
> > To unsubscribe from this group, send email to
> > osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsu...@googlegroups.com>
>
> --
> $*jagmohan sharma*$

varsha bhavnani

unread,
Jun 23, 2010, 6:23:59 AM6/23/10
to osdd-c...@googlegroups.com
http://spreadsheets.google.com/ccc?key=0AkKaURo7T-SGdDNsR2RDYXE4dGRNcWtESEtNSnNPUGc&hl=en#gid=0
this is the link
Varsha A. Bhavnani.
Research Scholar.
C/O Prof. J.K. Pal.
Cell & Molecular Biology Lab,
Dept of Biotechnology,
University of Pune,Pune.

JHAN P

unread,
Jun 23, 2010, 5:07:27 AM6/23/10
to osdd-c...@googlegroups.com
i am unable to include my name in the spreadsheet sir

varsha bhavnani

unread,
Jun 23, 2010, 6:20:01 AM6/23/10
to osdd-c...@googlegroups.com
On Wed, Jun 23, 2010 at 3:03 PM, jagmohan sharma <jagmohans...@gmail.com> wrote:
how to include subfield.....
jst go on this site and see if u ave the access after logging in.
if u r able to log in u will be able to see your name in the list.
jst enter  subfield in front of ur name.



--

lekha.y

unread,
Jun 23, 2010, 8:59:46 AM6/23/10
to osdd-c...@googlegroups.com
Respected Sir,
                     i successfully installed cdk descriptor in vista.
                     i gave the sample sdf file as input file.
                    and i got  outfile in the .txt format.
                    i attached my output file.please tell me what i got in the output file is correct or not .
                    how to infer the results from this output file.
                           thanking you.

--
*******************************************
LEKHA.Y,
IV  B.Tech Bioinformatics,
Center for Plant Molecular Biology (CPMB),
TamilNadu Agricultural University,
India.



sdf.txt.txt
CID_1752.sdf

jagmohan sharma

unread,
Jun 23, 2010, 9:15:10 AM6/23/10
to osdd-c...@googlegroups.com
hello,

my name is there in the list but i m not able to write the subfield on this spread sheet.hv u done it..........
B.Tech Bioinformatics
VITU vellore

bansi

unread,
Jun 23, 2010, 9:20:53 AM6/23/10
to osdd-c...@googlegroups.com
i am alsonot able to write subfield


 
On Tue, Jun 22, 2010 at 9:31 AM, Vinod Scaria <vin...@igib.in> wrote:

bansi

unread,
Jun 23, 2010, 9:13:39 AM6/23/10
to osdd-c...@googlegroups.com
sir i tried to do download it its nt downling

On Tue, Jun 22, 2010 at 9:31 AM, Vinod Scaria <vin...@igib.in> wrote:

tina bhattacharya

unread,
Jun 23, 2010, 12:51:53 PM6/23/10
to osdd-c...@googlegroups.com
sir,
i am unable to include my name in the spreadsheet....plz help me sir.....waitin for your reply...

sudeshna

subha sree.C.R.

unread,
Jun 23, 2010, 12:53:11 PM6/23/10
to osdd-c...@googlegroups.com
Sir I am unable to include my name and email ID and my sub-area in the master spreadsheet
 
http://spreadsheets.google.com/ccc?key=0AkKaURo7T-SGdDNsR2RDYXE4dGRNcWtESEtNSnNPUGc&hl=en#gid=0

my name is: c.r.subhasree@subha

email id: c.r.su...@gmail.com

sub area: cheminformatics



On Tue, Jun 22, 2010 at 9:31 AM, Vinod Scaria <vin...@igib.in> wrote:
--
You received this message because you are subscribed to the Google
Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
To post to this group, send email to osdd-c...@googlegroups.com
To unsubscribe from this group, send email to
osdd-cheminf...@googlegroups.com



--
Subhasree C.R.
II M.Sc Bioinformatics
University of Madras
Guindy campus

Teja Colluru

unread,
Jun 23, 2010, 1:29:59 PM6/23/10
to osdd-c...@googlegroups.com
Hi,

You have to sign in. Check the top right corner. Sign into google docs and look for your mail id in the spreadsheet. It will already be there if you have subscribed to this google group. Just enter your field of interest.

Regards,
Teja


tina bhattacharya

unread,
Jun 23, 2010, 11:45:18 PM6/23/10
to osdd-c...@googlegroups.com


tnx teja......hav successfully added my area f interest.

Nama

unread,
Jun 24, 2010, 5:11:34 AM6/24/10
to osdd-c...@googlegroups.com
Hi,

I have the same query.
I have downloaded .sdf file but don't know what does it contain?

I am not getting output file after running this jar file.
Plz let me know how to infer from output file after running the tool which is very imp aspect.

Namrata.

2010/6/23 lekha.y <induja...@gmail.com>



--
Not getting what you want is sometimes a wonderful stroke of luck....


jaleel uc

unread,
Jun 24, 2010, 6:14:09 AM6/24/10
to osdd-c...@googlegroups.com
can u come online or call  skype or gmail
Dr U.C.A.Jaleel.
Asst Professor in cheminformatics
Cheminformatics Division( UGC)
Malabar Christian College
Calicut University

shreya chakraborty

unread,
Jun 24, 2010, 6:31:42 AM6/24/10
to osdd-c...@googlegroups.com
Respected sir,
                I have downloaded and installed CDK calculator.Now my query is whether i have to install ANT and Eclipse for CDK library.
thanking you,
Shreya Chakraborty
Project Assistant
OSDD-IGIB

ankhi das

unread,
Jun 24, 2010, 6:09:18 AM6/24/10
to osdd-c...@googlegroups.com
Nmrata,
          For output file you open a notepad and save it. then take the blank notepad as output file. when CDK calculation is completed then it print the result on that blank notepad.
       Ankhi

On Thu, Jun 24, 2010 at 2:41 PM, Nama <namrat...@gmail.com> wrote:

Nama

unread,
Jun 24, 2010, 6:19:47 AM6/24/10
to osdd-c...@googlegroups.com
M online thru  gmail chat.
Namrata.

On Thu, Jun 24, 2010 at 3:44 PM, jaleel uc <jale...@gmail.com> wrote:

Nama

unread,
Jun 24, 2010, 7:38:17 AM6/24/10
to osdd-c...@googlegroups.com
Prob solved.
Thnx 4 help.

Namrata.

jaleel uc

unread,
Jun 25, 2010, 12:06:40 AM6/25/10
to osdd-c...@googlegroups.com
no
 
please refer u tube or post

nandha

unread,
Jun 30, 2010, 7:16:59 AM6/30/10
to OSDD Cheminformatics, jaleel...@gmail.com
Dear Sir,

I am unable to include my name and email ID and my sub-area in the
master spreadsheet.
Name : nandha devi
gmail id : nand...@gmail.com


On Jun 25, 9:06 am, jaleel uc <jaleel...@gmail.com> wrote:
> no
>
> please refer u tube or post
>
> On 6/24/10, shreya chakraborty <chakraborty.bobb...@gmail.com> wrote:
>
>
>
>
>
>
>
> > Respected sir,
> >                 I have downloaded and installed CDK calculator.Now my query
> > is whether i have to install ANT and Eclipse for CDK library.
> > thanking you,
> > Shreya Chakraborty
> > Project Assistant
> > OSDD-IGIB
>
> > On Thu, Jun 24, 2010 at 3:44 PM, jaleel uc <jaleel...@gmail.com> wrote:
>
> >> can u come online or call  skype or gmail
>
> >> On Thu, Jun 24, 2010 at 2:41 PM, Nama <namrata.to...@gmail.com> wrote:
>
> >>> Hi,
>
> >>> I have the same query.
> >>> I have downloaded .sdf file but don't know what does it contain?
>
> >>> I am not getting output file after running this jar file.
> >>> Plz let me know how to infer from output file after running the tool
> >>> which is very imp aspect.
>
> >>> Namrata.
>
> >>> 2010/6/23 lekha.y <indujayuva...@gmail.com>
>
> >>>> Respected Sir,
> >>>>                      i successfully installed cdk descriptor in vista.
> >>>>                      i gave the sample sdf file as input file.
> >>>>                     and i got  outfile in the .txt format.
> >>>>                     i attached my output file.please tell me what i got
> >>>> in the output file is correct or not .
> >>>>                     how to infer the results from this output file.
> >>>>                            thanking you.
>
> >>>>> > >> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
> >>>>> <osdd-cheminfo%2Bunsu...@googlegroups.com<osdd-cheminfo%252Bunsubscribe­@googlegroups.com>
>
> >>>>> > > --
> >>>>> > > T.Suma
> >>>>> > > Project Associate
> >>>>> > > c/o Dr.Sharmistha Banerjee
> >>>>> > > Asst. Prof., Department of Biochemistry
> >>>>> > > &
> >>>>> > > c/o Dr.Niyaz Ahmed
> >>>>> > > Reader, Department of Biotechnology,
> >>>>> > > School of Life Sciences,
> >>>>> > > University of Hyderabad,
> >>>>> > > INDIA
>
> >>>>> > >  --
>
> >>>>> > > You received this message because you are subscribed to the Google
> >>>>> > > Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> >>>>> > > To post to this group, send email to
> >>>>> osdd-c...@googlegroups.com
> >>>>> > > To unsubscribe from this group, send email to
>
> >>>>> > > osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
> >>>>> <osdd-cheminfo%2Bunsu...@googlegroups.com<osdd-cheminfo%252Bunsubscribe­@googlegroups.com>
>
> >>>>> > --
> >>>>> > $*jagmohan sharma*$
>
> >>>>> --
>
> >>>>> You received this message because you are subscribed to the Google
> >>>>> Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> >>>>> To post to this group, send email to osdd-c...@googlegroups.com
> >>>>> To unsubscribe from this group, send email to
> >>>>> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
>
> >>>> --
> >>>> *******************************************
> >>>> LEKHA.Y,
> >>>> IV  B.Tech Bioinformatics,
> >>>> Center for Plant Molecular Biology (CPMB),
> >>>> TamilNadu Agricultural University,
> >>>> India.
>
> >>>> --
> >>>> You received this message because you are subscribed to the Google
> >>>> Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> >>>> To post to this group, send email to osdd-c...@googlegroups.com
> >>>> To unsubscribe from this group, send email to
> >>>> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
>
> >>> --
> >>> Not getting what you want is sometimes a wonderful stroke of luck....
>
> >>> --
> >>> You received this message because you are subscribed to the Google
> >>> Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> >>> To post to this group, send email to osdd-c...@googlegroups.com
> >>> To unsubscribe from this group, send email to
> >>> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
>
> >> --
> >> Dr U.C.A.Jaleel.
> >> Asst Professor in cheminformatics
> >> Cheminformatics Division( UGC)
> >> Malabar Christian College
> >> Calicut University
>
> >> --
> >>  You received this message because you are subscribed to the Google
> >> Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> >> To post to this group, send email to osdd-c...@googlegroups.com
> >> To unsubscribe from this group, send email to
> >> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
>
> > --
> > You received this message because you are subscribed to the Google
> > Groups "OSDD Cheminformatics" group [http://c2d.osdd.net].
> > To post to this group, send email to osdd-c...@googlegroups.com
> > To unsubscribe from this group, send email to
> > osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsubscribe@goog­legroups.com>
>
> --
> Dr U.C.A.Jaleel.
> Asst Professor in cheminformatics
> Cheminformatics Division( UGC)
> Malabar Christian College
> Calicut University- Hide quoted text -
>
> - Show quoted text -

nidhi gupta

unread,
Jul 1, 2010, 1:35:59 AM7/1/10
to osdd-c...@googlegroups.com
sir i am done with assignment 0 & assignment one. Now what we have to do

regards 
Nidhi Gupta
MS University
Baroda
Gujarat

On Tue, Jun 22, 2010 at 9:31 AM, Vinod Scaria <vin...@igib.in> wrote:

rivi verma

unread,
Jun 30, 2010, 11:53:11 AM6/30/10
to osdd-c...@googlegroups.com
Sign in first to get an access to master sheet.
--
Rivi Verma
M.Sc Systems Biology & Bioinformatics
Panjab University, Chandigarh.

patterson

unread,
Jul 5, 2010, 5:43:20 AM7/5/10
to OSDD Cheminformatics
Hello Everybody...
My Id i misspelt so couldn gain access to the spreadsheet...
its spelt atfo...@gmail.com instead of patf...@gmail.com..
Somebody help me with this



On Jun 30, 4:16 pm, nandha <nandhu...@gmail.com> wrote:
> Dear Sir,
>
>  I am unable to include my name and email ID and my sub-area in the
> master spreadsheet.
>  Name : nandha devi
> gmail id : nandhu...@gmail.com

jaleel uc

unread,
Jul 5, 2010, 5:50:21 AM7/5/10
to osdd-c...@googlegroups.com
please sign in and try to enter

Vinod Scaria

unread,
Jul 5, 2010, 7:19:31 AM7/5/10
to osdd-c...@googlegroups.com
I will add the correct mail and provide access.

Vinod

--
Sent from my mobile device

suri sowmya

unread,
Jul 5, 2010, 7:21:18 AM7/5/10