ASSIGNMENT 0

[Vinod Scaria]

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

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[Amit Kumar Singh]

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]

sir, i want to know how to get a input and output file for CDK

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[Suma Avasthi]

unable to include my name too in the spreadsheets sir
T.Suma Avasthi
chemiinformatics
sumaa...@gmail.com

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--
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]

how to include subfield.....

$*jagmohan sharma*$

[vinod kumar]

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]

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]

i am unable to include my name in the spreadsheet sir

[varsha bhavnani]

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.

http://spreadsheets.google.com/ccc?key=0AkKaURo7T-SGdDNsR2RDYXE4dGRNcWtESEtNSnNPUGc&hl=en#gid=0

--

[lekha.y]

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.

[jagmohan sharma]

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]

i am alsonot able to write subfield

 

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

[bansi]

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]

sir,
i am unable to include my name in the spreadsheet....plz help me sir.....waitin for your reply...

sudeshna

[subha sree.C.R.]

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:

--
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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]

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]

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

[Nama]

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]

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]

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]

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]

M online thru  gmail chat.
Namrata.

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

[Nama]

Prob solved.
Thnx 4 help.

Namrata.

[jaleel uc]

no

 

please refer u tube or post

[nandha]

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]

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]

Sign in first to get an access to master sheet.

--
Rivi Verma
M.Sc Systems Biology & Bioinformatics
Panjab University, Chandigarh.

[patterson]

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]

please sign in and try to enter

[Vinod Scaria]

I will add the correct mail and provide access.

Vinod

--
Sent from my mobile device

[suri sowmya]

Sir gudevenin,

Im done with 1st assignment.......so wat is the next step that I have to do?.....Plz let me know sir

Thanks & Regards
Sowmya.S

[suri sowmya]

Goodevening Sir,

I want to change my group from cheminformatics to datacuration02  Cloning, Expression & Purification of Mtb Proteins . I have applied for the group, but, the request is still pending. Could you please help me sir?

On Mon, Jul 5, 2010 at 4:49 PM, Vinod Scaria <vin...@igib.in> wrote:

--
Thanks & Regards
Sowmya.S

[jaleel uc]

it is already reported 

[yogesh khandokar]

Dear Vinod Sir,

 

I have small query about the CDK software.

 

What is the minimum requirement of Computer memory and speed to perform the CDK experiment with 100 compounds

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

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


--

--
Yogesh Khandokar
JRF
Protein Crystallography Lab.,
National Institute of Immunology,
New Delhi.
India

[sumit joshi]

respected sir
which video you upload of weka is very good please upload more

@193@

[nidhi gupta]

respected sir

my name is nidhi and my id is nidhi....@gmail.com

thanks and regards

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

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


--

[GAURAV]

i am unable to include my name in the spreadsheet sir
GAURAV JOSHI
always be happy
byee and take care.

[rivi verma]

Gaurav

Sign in before in the mastersheet. u will find ur name there if u r a member of osdd means if u have already registered youself in this project.

[GAURAV]

thanx rivi 4 ur kind help

GAURAV JOSHI
always be happy
byee and take care.

[NAGARAJAN]

Hello sir

I have completed both cdk and weka projects and edited in the
spreed sheet as "DONE" to my mail id. But till now the group was not
assigned. Please assign a group for me to continue the work.

I have mistakenly send my mail id to you ( Vinod scaria). He added
again my name in spreed sheet. So please remove my repeated mail id in
the 194 th position and keep the 33rd position mail id.

Thank you
with great enthusiasm
R.Nagarajan

On 7/15/10, GAURAV <gjos...@gmail.com> wrote:
> thanx rivi 4 ur kind help
> GAURAV JOSHI
> always be happy
> byee and take care.
>
>
> On Tue, Jul 13, 2010 at 10:02 PM, rivi verma <rivi....@gmail.com> wrote:
>
>> Gaurav

>> *Sign in* before in the mastersheet. u will find ur name there if u r a

>>>> osdd-cheminf...@googlegroups.com<osdd-cheminfo%2Bunsu...@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%2Bunsu...@googlegroups.com>

>>>
>>
>>
>>
>> --
>> Rivi Verma
>> M.Sc Systems Biology & Bioinformatics
>> Panjab University, Chandigarh.
>>
>> --
>> 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>

>>
>
> --
> 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
>

--
*****************************
R.NAGARAJAN
II M.Sc Bioinformatics
Bharathidasan University
Tiruchirappalli.
****************************

[Muhammad nk]

I also inters in work but how to access (How to include my ID And e-
mail)

[vijay rathod]

Hello sir

 

   I have completed both cdk and weka projects and edited in thespreed sheet

 as "DONE" to my mail  id but  i completed it very late afetr theassigning the

groups this is due to the the inconvinience in the getting the  video tutorials  and

and running the softwares on my pc   .Please assign a group for me to continue

the work

 

thanking you 

 

 

On Sun, Aug 8, 2010 at 4:17 PM, Muhammad nk <abcr...@gmail.com> wrote:

> I also inters in work but how to access (How to include my ID And e-

> mail)

>

> --

> 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

>

 

 

 

--

Vijay  Rathod

M.S.Pharmacoinformatics

Centre of Pharmacoinformatics

NIPER(Mohali)

Punjab 160 062