scaffoldhunter-users Mailing List for Scaffold Hunter (Page 3)

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Hi Nils,

Thanks a lot for pointing me towards the approach, I will let you know
once I'm done with the proposal .Please do guide me anything necessary
meanwhile .

Thanks,
Srikanth.

hi,
thanks for clarifying the doubt .I am going through the hibernate part and
now i can proceed with my proposal.
regards,
Prateek

On Thu, Apr 25, 2013 at 3:42 PM, <nl...@us...> wrote:

> Hi Prateek,
>
> On Thursday 25 April 2013 14:09:05 Prateek Gupta wrote:
> > well currently I have prepared an algorithm for embedding JChemPaint as
> > structure editor for the query.
> > but I need to ask that JChemPaint saves and loads the editor structure in
> > CML and MDL mol format but only loads sdf format.
> > So I am employing a converter agent "obabel" so as to convert from CML to
> > sdf format.This sdf file can be used as dataset for the query.
> > Is there any discrepancy with this logic?
>
> OpenBabel is written in C++ and using it for a cross-platform Java
> application
> like Scaffold Hunter has several disadvantages. Moreover, there should be
> no
> need to introduce additional dependencies. JChemPaint is based on CDK and
> it
> is straightforward to load MDL mol files with CDK using the class MDLReader
> (see
>
> edu.udo.scaffoldhunter.model.datacalculation.DBMoleculeToCDKMoleculeTransform
> for example code). Basically SDF is a container format for MDL mol files.
>
>
> Regards,
>   Nils
>

Hi Prateek,

On Thursday 25 April 2013 14:09:05 Prateek Gupta wrote:
> well currently I have prepared an algorithm for embedding JChemPaint as
> structure editor for the query.
> but I need to ask that JChemPaint saves and loads the editor structure in
> CML and MDL mol format but only loads sdf format.
> So I am employing a converter agent "obabel" so as to convert from CML to
> sdf format.This sdf file can be used as dataset for the query.
> Is there any discrepancy with this logic?

OpenBabel is written in C++ and using it for a cross-platform Java application 
like Scaffold Hunter has several disadvantages. Moreover, there should be no 
need to introduce additional dependencies. JChemPaint is based on CDK and it 
is straightforward to load MDL mol files with CDK using the class MDLReader 
(see 
edu.udo.scaffoldhunter.model.datacalculation.DBMoleculeToCDKMoleculeTransform 
for example code). Basically SDF is a container format for MDL mol files.

Regards,
  Nils

or is there any other around the way method to use CML or MDL mol format
query directly ?

On Thu, Apr 25, 2013 at 2:09 PM, Prateek Gupta
<pra...@gm...>wrote:

> hi,
> well currently I have prepared an algorithm for embedding JChemPaint as
> structure editor for the query.
> but I need to ask that JChemPaint saves and loads the editor structure in
> CML and MDL mol format but only loads sdf format.
> So I am employing a converter agent "obabel" so as to convert from CML to
> sdf format.This sdf file can be used as dataset for the query.
> Is there any discrepancy with this logic?
>
> Also I am looking into the hibernate model for object -relation mapping
> and potential betterment.
>
>
> On Thu, Apr 25, 2013 at 1:31 PM, <nl...@us...> wrote:
>
>> Hi Prateek,
>>
>> On Thursday 25 April 2013 12:17:59 Prateek Gupta wrote:
>> > I also used the 2.2 version of the scaffolhunter software.I came across
>> > multiple differences between the 1.7 to 2.2 version.
>> > I understood my previous doubts after using the software more
>> thoroughly.
>> > But I want to what exactly is meant by
>> > "calculation of fingerprints for effective filtering as well as a
>> subgraph
>> > isomorphism algorithm for validation, but lacks integration in the
>> current
>> > filtering framework" .
>> > What are the discrepancies that are targetted.
>>
>> as you have seen, the current filtering framework is slightly different
>> from
>> the one used in the previous releases (v1.x). Another difference is that
>> the
>> new version uses Hibernate for object-relational mapping and is more
>> independent of the database server used. However, this level of
>> abstraction
>> might prohibit some (MySQL-specific) database queries used in the previous
>> version. For example, the filtering based on bit operations on the
>> database
>> site might be problematic. A good approach should be compatible with most
>> database servers while still being as efficient as possible. This
>> requires to
>> investigate the operations supported by Hibernate and it might also help
>> to do
>> some test runs first to come up with feasible practical solution.
>>
>>
>> Regards
>>   Nils
>>
>>
>> ------------------------------------------------------------------------------
>> Try New Relic Now & We'll Send You this Cool Shirt
>> New Relic is the only SaaS-based application performance monitoring
>> service
>> that delivers powerful full stack analytics. Optimize and monitor your
>> browser, app, & servers with just a few lines of code. Try New Relic
>> and get this awesome Nerd Life shirt!
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>> _______________________________________________
>> Scaffoldhunter-users mailing list
>> Sca...@li...
>> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
>>
>
>

hi,
well currently I have prepared an algorithm for embedding JChemPaint as
structure editor for the query.
but I need to ask that JChemPaint saves and loads the editor structure in
CML and MDL mol format but only loads sdf format.
So I am employing a converter agent "obabel" so as to convert from CML to
sdf format.This sdf file can be used as dataset for the query.
Is there any discrepancy with this logic?

Also I am looking into the hibernate model for object -relation mapping and
potential betterment.

On Thu, Apr 25, 2013 at 1:31 PM, <nl...@us...> wrote:

> Hi Prateek,
>
> On Thursday 25 April 2013 12:17:59 Prateek Gupta wrote:
> > I also used the 2.2 version of the scaffolhunter software.I came across
> > multiple differences between the 1.7 to 2.2 version.
> > I understood my previous doubts after using the software more thoroughly.
> > But I want to what exactly is meant by
> > "calculation of fingerprints for effective filtering as well as a
> subgraph
> > isomorphism algorithm for validation, but lacks integration in the
> current
> > filtering framework" .
> > What are the discrepancies that are targetted.
>
> as you have seen, the current filtering framework is slightly different
> from
> the one used in the previous releases (v1.x). Another difference is that
> the
> new version uses Hibernate for object-relational mapping and is more
> independent of the database server used. However, this level of abstraction
> might prohibit some (MySQL-specific) database queries used in the previous
> version. For example, the filtering based on bit operations on the database
> site might be problematic. A good approach should be compatible with most
> database servers while still being as efficient as possible. This requires
> to
> investigate the operations supported by Hibernate and it might also help
> to do
> some test runs first to come up with feasible practical solution.
>
>
> Regards
>   Nils
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> Scaffoldhunter-users mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
>

Hi Prateek,

On Thursday 25 April 2013 12:17:59 Prateek Gupta wrote:
> I also used the 2.2 version of the scaffolhunter software.I came across
> multiple differences between the 1.7 to 2.2 version.
> I understood my previous doubts after using the software more thoroughly.
> But I want to what exactly is meant by
> "calculation of fingerprints for effective filtering as well as a subgraph
> isomorphism algorithm for validation, but lacks integration in the current
> filtering framework" .
> What are the discrepancies that are targetted.

as you have seen, the current filtering framework is slightly different from 
the one used in the previous releases (v1.x). Another difference is that the 
new version uses Hibernate for object-relational mapping and is more 
independent of the database server used. However, this level of abstraction 
might prohibit some (MySQL-specific) database queries used in the previous 
version. For example, the filtering based on bit operations on the database 
site might be problematic. A good approach should be compatible with most 
database servers while still being as efficient as possible. This requires to 
investigate the operations supported by Hibernate and it might also help to do 
some test runs first to come up with feasible practical solution.

Regards
  Nils

hi,
I also used the 2.2 version of the scaffolhunter software.I came across
multiple differences between the 1.7 to 2.2 version.
I understood my previous doubts after using the software more thoroughly.
But I want to what exactly is meant by
"calculation of fingerprints for effective filtering as well as a subgraph
isomorphism algorithm for validation, but lacks integration in the current
filtering framework" .
What are the discrepancies that are targetted.
Apart from this the Jchempaint integration as structure editor is fairly
understood.

On Wed, Apr 24, 2013 at 10:39 PM, Prateek Gupta <pra...@gm...
> wrote:

> hi,
> sorry for the inconvinience for my last post not on the mailing list.
> By my last post I was trying to convey that which I have understood and to
> seek your opinion.
> I used the version 1.7 because it was pointed out in a previous mail.I
> will install the 2.x version soon.
> I have read the CT-index research paper and what i have learnt uptil now.
> By the subset reason I was trying to convey about the degree of
> fingerprint matching of the features of the query pattern with the features
> of the database graph pattern.Those that were positive in the test were
> used for the isomorphism procedure and discarding the rest.
> This is the string matching algorithm that is being used in the formal
> definition of certificate matching?
>
> So I aim to know what exactly does the fragment z value that is currently
> limited to 0-6 accounts for in the filter rules  .Is it the number of
> features to be taken into account while filtering or the number of atoms
> that must be possessed in the drug compound , of the query atom that filter
> mechanism is  considering or is it related to the fingerprinting bit array?
>
> Also does this project idea aims to integrate the JChemPaint as the new
> editor over the current structure editor being used.
>
> Regards,
> Prateek
>
>

hi,
sorry for the inconvinience for my last post not on the mailing list.
By my last post I was trying to convey that which I have understood and to
seek your opinion.
I used the version 1.7 because it was pointed out in a previous mail.I will
install the 2.x version soon.
I have read the CT-index research paper and what i have learnt uptil now.
By the subset reason I was trying to convey about the degree of fingerprint
matching of the features of the query pattern with the features of the
database graph pattern.Those that were positive in the test were used for
the isomorphism procedure and discarding the rest.
This is the string matching algorithm that is being used in the formal
definition of certificate matching?

So I aim to know what exactly does the fragment z value that is currently
limited to 0-6 accounts for in the filter rules  .Is it the number of
features to be taken into account while filtering or the number of atoms
that must be possessed in the drug compound , of the query atom that filter
mechanism is  considering or is it related to the fingerprinting bit array?

Also does this project idea aims to integrate the JChemPaint as the new
editor over the current structure editor being used.

Regards,
Prateek

Dear Prateek,
first i would like to ask you to write your questions using the mailing list sca...@li...
for further questions. This allows us to answer questions only once and do not repeat ourself for other students.

Am 24.04.2013 15:39, schrieb Prateek Gupta:
> hi,
> I used the scaffold hunter project with the dataset after creating the database in the mysql server.
> uptil now , I am able to understand that the idea that I want to work on ,"substructure search" ,involves the filtering
> framework.
> I am briefing you my understanding and if any discrepancy please help me understand that.
> 1)After selecting the "overview over the scaffold property" , which basically targets the atom about which the filter
> framework has to work ,
> 2) proceeds to the "definition of the filter rules" ,which seeks user input as to the number of subsets that it should
> create of the compound >,=,< ,
> 3) then proceeds to substructure part , where substructure can be edited and when the option search scaffold is selected
> it analyses the compound and displays the result.
> 
> Does this project idea supposedly aims to seek user input in terms of the number of subsets that the compound needs to
> be segregated into and also about the integration of JChemPaint editor in the project!
> Can you help me in more understanding about the different filter rules applied.About the ">" , " =" , " <" options usage
> and target!

I do not know if i understood you right, but i will try to give you an answer based on what i understood. Please note
that the 1.7 Version which contains an implementation of the substructure filtering is very different from the current
version (2.x) regarding the handling of filtering in general. In general filtering is not meant to distribute a number
of molecules into different subsets but to reduce a subset by keeping only the molecules which match a set of filter
rules. For the general understanding of sets/subsets and filtering please refer to section 6.2 of the Scaffold Hunters
manual, which is part of the distributed zip-file.

Regards
Till

> And about the current editor being used in the project
> 
> Also the overall requirements of the project idea as I am starting to build my proposal and need to understand it.
> 
> Regards,
> Prateek.
> 
> 
> On Tue, Apr 16, 2013 at 2:18 AM, Nils Kriege <nil...@tu... <mailto:nil...@tu...>> wrote:
> 
>     Hi Prateek,
> 
>     did you receive my reply regarding your questions via the mailing list? In
>     case you subscribed to the list later, you can find my reply here:
> 
>     https://sourceforge.net/mailarchive/message.php?msg_id=30711483
> 
>     The project is not about implementing or improving the CT-Index approach, the
>     goal is a user-friendly integration of the existing CT-Index implementation in
>     Scaffold Hunter. Unfortunately, the term "filtering" is ambiguous: There is a
>     filtering framework in Scaffold Hunter which basically allows to create
>     subsets of compound sets by specifying rules like "all molecules with property
>     x < 7". We would like to support rules like "all molecules that contain
>     fragment z". These queries can be answered by means of CT-Index, which uses
>     fingerprint-based filtering for efficiency.
> 
> 
>     Regards
>     Nils
> 
>     On Tuesday 16 April 2013 05:26:16 Karsten Klein wrote:
>     > -------- Original-Nachricht --------
>     > Betreff:      Re: [Scaffoldhunter-users] Introduction
>     > Datum:        Mon, 15 Apr 2013 21:37:49 +0530
>     > Von:  Prateek Gupta <pra...@gm... <mailto:pra...@gm...>>
>     > An:   Karsten Klein <kar...@ud... <mailto:kar...@ud...>>
>     >
>     >
>     >
>     > hi Karsten,
>     > i have subscribed to the user and developer mailing list but there seems
>     > no activity and response.
>     > II went through the paper
>     > CT-Index: Fingerprint-based Graph Indexing Combining Cycles and Trees
>     > <http://dx.doi.org/10.1109/ICDE.2011.5767909>
>     > and tried to understand the implementation algorithm and preparing to
>     > use the software jchempaint.
>     > As for the lack in integration of the filtering technique,does the
>     > project idea aims to implement a new
>     > algorithm or is it to make the current algorithm more efficient?
>     >
>     >
>     > On Thu, Apr 11, 2013 at 5:02 PM, Karsten Klein <kar...@ud... <mailto:kar...@ud...>
>     > <mailto:kar...@ud... <mailto:kar...@ud...>>> wrote:
>     >
>     >     Hi Prateek,
>     >
>     >     as the discussion might help others too to understand a bit more what
>     >     the project is about, or some potential mentor might want to
>     >     comment, yes.
>     >
>     >         Karsten
> 
> 

-- 
Dipl.-Inf. Till Schäfer
Technische Universität Dortmund
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14
44227 Dortmund, Germany

e-mail: til...@cs...
phone: +49(231)755-7706
fax: +49(231)755-7740
web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
pgp: https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79

Hi Srikanth,

SAR is a very general term. It might be more useful to search for "SAR table", 
"SAR Map" or "R-Group table" to get an idea of the concept and variations.

A straight forward approach is to start with a SAR table for a single 
scaffold. Each row represents a molecule and there are columns for each 
substitution site and each property of the molecule. This would already be 
very useful when linked to the Scaffold Tree View.
However, the problem becomes more challenging when molecules with different 
scaffolds should be depicted in the same table. The second article (Clark & 
Labute) listed at the ideas page deals with this problem from the molecular 
structure point of view. However, I think a less sophisticated approach should 
be sufficient for the project idea. You may think about the following  
challenging questions:

  * Is there a viable simple approach to assign scaffolds/substitution sites
    for the case of molecules with different scaffolds? An approach different
    from the one described in the article would be to identify a common core
    of all molecules (e.g., based on their maximum common subgraph, a
    functionality provided by the toolkit CDK). However, this is computational
    demanding and the core typically does not comply with the scaffolds
    contained in the scaffold tree view. Can views be linked in a meaningful
    way in this case?

  * Assume only scaffolds according to the scaffold tree are generated and one
    scaffold is an ancestor of a different scaffold in the tree. Can this 
    relation be visualized in the SAR table view? Can both views be linked in
    a way such that their relation becomes clear?

  * If we have multiple scaffolds and multiple substitution sites, how to
    visualize them in one table? One approach would be to generate a table,
    where each row represents a scaffold and each column a specific substitute
    for a single user-selected substitution site. Then each cell may represent 
    multiple molecules (differing at the other substitution sites). How to
    visualize the property values of multiple molecules in one cell?

Regards,

  Nils

On Tuesday 23 April 2013 11:44:56 srikanth bezawada wrote:
> Hello Karsten and Nils, Thanks for your reply!
> 
> 
>         Karsten, I have started exploring more about SAR to get
> familiar with it and I'll post if I get doubts . Please do point me
> any more specific links if I should refer  regarding SAR. Once I'm
> done with basics of SAR, we can discuss regarding how end user must
> visualize (or) work with the table view.
> 
>         Nils, Thanks for pointing me towards required sourcecode to be
> concentrated upon. Since the project idea is straight forward, what
> key points can i include in my proposal, so as to send ahead something
> strong and concrete ? .
> 
> 
> 
> Thanks,
> Srikanth.

Hello, everybody.

My name is Shi Xiaolong. I'm a student from China. I'm willing to implement the idea
"Ramachandran Plots, Treemaps, and Heatmaps"

Now , I'll introduce myself. I'm a graduate student at Peking University ,one of 
the top universities in China, majoring Computer Science. I recieve my bacheler in 
Beijing Institute of Technology majoring Computer Science too. I have used C and C
++ over four years . I have laid a solid foundation of Computer Science and I love 
coding and studying. In my spare time, I also study Python, Java ,Matlab and Processing.

My research field is computer graphics and information visualization. I have basic knowledge
of them. I love visualization. Making data visible is a great thing for users including scientists. 
Visualization is a tool to find the pattern among the data. I have done research on 2D vector
field visualization. I think I can complete the task and make a contribution to the open source 
community and Scaffold Hunter.

Shi Xiaolong
Hello Karsten and Nils, Thanks for your reply!

        Karsten, I have started exploring more about SAR to get
familiar with it and I'll post if I get doubts . Please do point me
any more specific links if I should refer  regarding SAR. Once I'm
done with basics of SAR, we can discuss regarding how end user must
visualize (or) work with the table view.

        Nils, Thanks for pointing me towards required sourcecode to be
concentrated upon. Since the project idea is straight forward, what
key points can i include in my proposal, so as to send ahead something
strong and concrete ? .

Thanks,
Srikanth.

Hi Srikanth,

Karsten's pointers are definitely a good starting point.

On Sunday 21 April 2013 14:26:19 srikanth bezawada wrote:
> I would like to get pointed
> towards more resources other than literature,any extra explanations needed
> regarding this project so that I can start working.Also,please do point me
> towards the documentation for the source code 2.2.0 .

A Javadoc documentation can be generated using the ant build file contained in 
the repository. You can check out trunk and build it by the command "ant 
javadoc".
There are two packages of special interest for the project idea "Structure-
Activity relationship": edu.udo.scaffoldhunter.model.treegen contains code 
implementing the cheminformatics technique, i.e., generating scaffolds by 
pruning side chains. This functionality is currently used in a preprocessing 
step. However, for the project idea it is more appropriate to generate the 
scaffolds when they are required for the SAR view and to keep track of the 
side chains pruned. There is no need to support very large data sets (with 
thousands of scaffolds) for the SAR table view.
To implement a new view the package edu.udo.scaffoldhunter.view is important, 
it contains the interfaces that have to be implemented.

Regards
Nils

Hi,

we have recently added a sample data set and a short guide to help you to get 
started quickly with Scaffold Hunter. This should also help GSoC participants 
interested in Scaffold Hunter to try out the software and get a better idea of 
the projects proposed.

The data set is available for download from 
https://sourceforge.net/projects/scaffoldhunter/files/datasets/

Regards
Nils

Hi Vlad,

thank you for your emails. What we are looking for basically are people
that have the necessary prerequisites, are willing to learn new things,
and are interested in improving Scaffold Hunter.

In the end we want the student to learn something in a successful
project that provides improvement to our tool.

So in general you should make sure we know about your skills and any
specific knowledge that might help in successfully completing the
project (without overdoing, of course ;-)).
In addition, it helps to show that you are actively thinking about
the project, and that you prepare a concept to deal with the challenge.
This could be either to ask specific questions on the realization, or
to propose a plan how you think you will tackle the problem.

Best,
    Karsten

Am 23.04.2013 16:18, schrieb Karsten Klein:
> Forwarded this email as topics might be of interest for others, too:
> 
> 
> Hi.
> 
> Thanks a lot for the response and for the data example. I've gone
> through the application, read the manual and also took a look at
> piccolo(which I think I'll use for my next Software Design assignment).
> I find the views very interesting. I particularly liked how after
> zooming in close enough the structures become visible both in the
> dendrogram and scaffold tree and I also think the detailed view in table
> is very useful.
> I'm really excited that I could learn things that are not in my area of
> study this summer(for example I had no idea about SMILES) so what I'd
> like to know, of course, is how I can improve my chances of being
> accepted for your project.
> 
> Thank you,
> Vlad.
> 
> 2013/4/18 Nils Kriege <nil...@tu...
> <mailto:nil...@tu...>>
> 
>     Hi Vlad,
> 
>     thanks for your interest in Scaffold Hunter. I have uploaded a
>     sample dataset:
>     https://sourceforge.net/projects/scaffoldhunter/files/datasets/
> 
>     I will add a more detailed description of the dataset and how to
>     import it
>     later. However, starting Scaffold Hunter and importing the SDF file is
>     straight-forward and allows you to find out more about the
>     application and the
>     different views it currently supports.
> 
>     Having a look at Piccolo is a good start, piccolo2d.org
>     <http://piccolo2d.org> provides a detailed
>     tutorial and the library comes with some nice code examples.
> 
>     I'm looking forward to hearing from you.
> 
> 
>     Regards
>     Nils
> 
> 
>     On Tuesday 16 April 2013 21:57:35 you wrote:
>     > Hi,
>     >
>     > My name is Vlad Topala and I'm currently in my third year of studying
>     > Computer Science at the Technical University of Cluj-Napoca. Also, in
>     > September, last year, I started working for Tora Trading Services
>     after a 3
>     > month internship. I work in Java, mainly front-end development
>     based on
>     > Swing and although I never thought I'd like developing GUI, it
>     gets more
>     > interesting each day :). I've worked with mercurial and git, maven
>     and ant
>     > and I have some basic SVN knowledge.
>     > Last weekend I found the Scaffold Hunter project on Google-melange
>     and from
>     > what I read I think it's really interesting so I thought it
>     wouldn't hurt
>     > to try and contact someone. I cloned the code and started to snoop
>     around.
>     > I managed to build and start the application but unfortunately did
>     not find
>     > a suitable database to test it on. The ideas I find most appealing
>     from the
>     > proposed ones are the implementation of a console interface and
>     the three
>     > ideas regarding Views. I also read that experience with piccolo
>     would be
>     > good so I'll start to experiment with it.
>     > What I would like to know first is are there any sample databases
>     I can
>     > test the application with? I'd really love to join you starting
>     this summer
>     > and of course I'd like to see the application running and to get a
>     better
>     > idea of all the implications.
>     >
>     > Thank you very much,
>     > Vlad Topala.
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service 
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> Scaffoldhunter-users mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> 

Forwarded this email as topics might be of interest for others, too:

Hi.

Thanks a lot for the response and for the data example. I've gone
through the application, read the manual and also took a look at
piccolo(which I think I'll use for my next Software Design assignment).
I find the views very interesting. I particularly liked how after
zooming in close enough the structures become visible both in the
dendrogram and scaffold tree and I also think the detailed view in table
is very useful.
I'm really excited that I could learn things that are not in my area of
study this summer(for example I had no idea about SMILES) so what I'd
like to know, of course, is how I can improve my chances of being
accepted for your project.

Thank you,
Vlad.

2013/4/18 Nils Kriege <nil...@tu...
<mailto:nil...@tu...>>

    Hi Vlad,

    thanks for your interest in Scaffold Hunter. I have uploaded a
    sample dataset:
    https://sourceforge.net/projects/scaffoldhunter/files/datasets/

    I will add a more detailed description of the dataset and how to
    import it
    later. However, starting Scaffold Hunter and importing the SDF file is
    straight-forward and allows you to find out more about the
    application and the
    different views it currently supports.

    Having a look at Piccolo is a good start, piccolo2d.org
    <http://piccolo2d.org> provides a detailed
    tutorial and the library comes with some nice code examples.

    I'm looking forward to hearing from you.

    Regards
    Nils

    On Tuesday 16 April 2013 21:57:35 you wrote:
    > Hi,
    >
    > My name is Vlad Topala and I'm currently in my third year of studying
    > Computer Science at the Technical University of Cluj-Napoca. Also, in
    > September, last year, I started working for Tora Trading Services
    after a 3
    > month internship. I work in Java, mainly front-end development
    based on
    > Swing and although I never thought I'd like developing GUI, it
    gets more
    > interesting each day :). I've worked with mercurial and git, maven
    and ant
    > and I have some basic SVN knowledge.
    > Last weekend I found the Scaffold Hunter project on Google-melange
    and from
    > what I read I think it's really interesting so I thought it
    wouldn't hurt
    > to try and contact someone. I cloned the code and started to snoop
    around.
    > I managed to build and start the application but unfortunately did
    not find
    > a suitable database to test it on. The ideas I find most appealing
    from the
    > proposed ones are the implementation of a console interface and
    the three
    > ideas regarding Views. I also read that experience with piccolo
    would be
    > good so I'll start to experiment with it.
    > What I would like to know first is are there any sample databases
    I can
    > test the application with? I'd really love to join you starting
    this summer
    > and of course I'd like to see the application running and to get a
    better
    > idea of all the implications.
    >
    > Thank you very much,
    > Vlad Topala.

Am 22.04.2013 07:26, schrieb srikanth bezawada:
> Hello mentors,
> 
>          I am Srikanth, a pre-final year student, currently
> pursuing /Information Systems //MSc Tech.// at / BITS-Pilani university,
> India. I am very interested in working in the field of information
> visualization. I have previously worked with Cytoscape which is an open
> source software helps in visualizing networks, mostly biological ones,
> as a part of one of my academic projects. I have downloaded Scaffold
> Hunter- 2.2.0 and currently playing around with it  using the manual. I
> am interested in* Structure-Activity relationship *project idea. I got
> the basic idea which is to integrate SAR tables into scaffold hunter as
> a seperate view. I would like to get pointed towards more resources
> other than literature,any extra explanations needed regarding this
> project so that I can start working.Also,please do point me towards the
> documentation for the source code 2.2.0 .
> 
> 
> 
> Thanks,
> Srikanth. 
> 
> 
> 
> * *
> 
> 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> 
> 
> 
> _______________________________________________
> Scaffoldhunter-users mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> 

Hi Srikanth,

welcome. Your Cytoscape experience definitely will help you.

For the SAR idea, it would be good to already have a look at the code
structure, and how the different views are integrated into the system.
Did you already have a look at the linked literature? It is important
to make yourself familiar with the way SAR is used by chemists.

Be aware that the papers are just examples, as there is a wealth of
literature on that topic out there. Feel free to further explore the
topic beyond those pointers.

You should have an idea what SAR tables are, understand
the underlying SAR concept, and think about your concept what is needed
to integrate those into Scaffold Hunter. This includes to check where
you can build upon the libraries and tools used already and if you would
need to add additional functionality to get a working SAR table.

A further point is the interaction allowed with the table, how
should the user be able to work with it, which operations need to be
supported.
I guess the assigned mentors will give some more information soon.

Regards,
    Karsten

Hello mentors,

         I am Srikanth, a pre-final year student, currently pursuing
*Information
Systems **MSc Tech.** at * BITS-Pilani university, India. I am very
interested in working in the field of information visualization. I have
previously worked with Cytoscape which is an open source software helps in
visualizing networks, mostly biological ones, as a part of one of my
academic projects. I have downloaded Scaffold Hunter- 2.2.0 and currently
playing around with it  using the manual. I am interested in*
Structure-Activity
relationship *project idea. I got the basic idea which is to integrate SAR
tables into scaffold hunter as a seperate view. I would like to get pointed
towards more resources other than literature,any extra explanations needed
regarding this project so that I can start working.Also,please do point me
towards the documentation for the source code 2.2.0 .

Thanks,
Srikanth.

* *

Hi Prateek,

On Wednesday 17 April 2013 21:25:21 Prateek Gupta wrote:
> I have understood some part of the literature and also trying to understand
> the required part of the source code for the filtering framework in the
> related modules.I want to know that does supporting rules like "all
> molecules that contain fragment z" implies to the containing of
> differentiating "features" (which are the hash-key in the CT-index method)
> of the molecules in the database mining search approach?

a query for all molecules that contain fragment z (where z is a user-specified 
structure) can be solved by CT-Index. The details of the approach like the 
fragments encoded by the hash-key fingerprint are not important for the 
project. JChemPaint should be integrated to specify the fragment z and CT-
Index should be used to answer the query.

>  Also But When trying to build jchempaint , I countinuously get the
> following error.
> 
> BUILD FAILED
> /home/prateek/Downloads/project/JChemPaint-jchempaint-b0b34cb/build.xml:711:
> /home/ralf/remote/CDK/jar does not exist.
> 
> What should i do?
> Cause I need to know how exactly and efficiently does jchempaint editor
> does it!

JChemPaint requires CDK, you may want to modify the file build.xml and adjust 
the path to your CDK library. Or refer to this page for further information on 
building JChemPaint:
https://github.com/JChemPaint/jchempaint/wiki/Development-jcp

Regards,
Nils

I have understood some part of the literature and also trying to understand
the required part of the source code for the filtering framework in the
related modules.I want to know that does supporting rules like "all
molecules that contain fragment z" implies to the containing of
differentiating "features" (which are the hash-key in the CT-index method)
of the molecules in the database mining search approach?

 Also But When trying to build jchempaint , I countinuously get the
following error.

BUILD FAILED
/home/prateek/Downloads/project/JChemPaint-jchempaint-b0b34cb/build.xml:711:
/home/ralf/remote/CDK/jar does not exist.

What should i do?
Cause I need to know how exactly and efficiently does jchempaint editor
does it!

On Mon, Apr 15, 2013 at 12:38 PM, Prateek Gupta <pra...@gm...
> wrote:

> hello,
> I am Prateek Gupta,IInd year student pursuing Bachelors in engineering
> with majors in computer science from BITS Pilani Goa,India.
> I am interested to participate in gsoc 2013 and interested in Scaffold
> Hunter organization.
> My skill set includes C,Java,python,mysql and android application
> development.
> I am interested in the idea substructure search in the ideas list.
>

hello,
I am Prateek Gupta,IInd year student pursuing Bachelors in engineering with
majors in computer science from BITS Pilani Goa,India.
I am interested to participate in gsoc 2013 and interested in Scaffold
Hunter organization.
My skill set includes C,Java,python,mysql and android application
development.
I am interested in the idea substructure search in the ideas list.

On Thursday 11 April 2013 01:23:29 Prateek Gupta wrote:
> http://dx.doi.org/10.1109/ICDE.2011.5767909
> this literature link asks for IEEE membership sign in.What should I do?

You should have received the paper by email.

Regards,
Nils

Hi Prateek,

thanks for your interest in Scaffold Hunter and the project idea "Substructure 
Search". Scaffold Hunter supports to filter data sets and the idea here is to 
allow the user to edit a molecular fragment with a structure editor and filter 
out all molecules that do not contain the fragment.

In a previous version of Scaffold Hunter this functionality was included by 
means of the editor JChemPaint. You may want to give version 1.7.1 a try to 
get an idea on how substructure search works. The source code of the old 
version can be found in the SVN repository located at tags/release-1.7.1.
The package subsearch contains the code implementing all basic functionality. 
The subpackages subsearch.graph, subsearch.index and subsearch.match are 
already ported to the code base of the current version version 2.1.3. You will 
find them in the package 
edu.udo.scaffoldhunter.model.filtering.subsearch.fingerprint in trunk.

Reintegrating the functionality in Scaffold Hunter requires to integrate a 
structure editor in the new filtering framework. JChemPaint [1] should be a 
good choice since it is based on the Chemitry Development Kit (CDK) [2] which 
is already used by Scaffold Hunter.
Filtering for substructure search is based on bit operations applied to 
fingerprints. As part of the project this should be implemented by database 
queries or on the client-side. Doing this by database queries is preferable 
for performance reasons. Therefore some experience with SQL databases and 
Hibernate [3] is an advantage.

Reading the paper "CT-Index" will give you some background knowledge on 
subgraph search techniques. However, it is not required to go into all 
details, since these parts are already implemented.

Regards,
Nils

[1] http://jchempaint.github.com/
[2] http://cdk.sourceforge.net/
[3] http://www.hibernate.org/

On Tuesday 09 April 2013 21:32:32 Prateek Gupta wrote:
> hello,
> I am Prateek Gupta,IInd year student pursuing Bachelors in engineering with
> majors in computer science from BITS Pilani Goa,India.
> I am interested to participate in gsoc 2013 and interested in Scaffold
> Hunter organization.
> My skill set includes C,Java,python,mysql and android application
> development.
> I am interested in the idea substructure search in the ideas list.
> If anyone could help me provide with the relative links for the further
> understanding of the idea and direct me with the requirements of the
> project?
> Thank you.

http://dx.doi.org/10.1109/ICDE.2011.5767909
this literature link asks for IEEE membership sign in.What should I do?

Hi Prateek,

thanks for your interest.
A good starting point would be to have a look at the linked paper (and
for further reading the literature cited there) to get a basic
understanding of the concepts underlying the algorithms that are
employed there, e.g. filter and verification. Then also a look at the
JChemPaint editor (or some suitable alternative) will help to get an
idea of what
a) the user interface will look like
b) kind of interfaces for data exchange etc. are provided

Regards,
    Karsten

Am 10.04.2013 02:02, schrieb Prateek Gupta:
> hello,
> I am Prateek Gupta,IInd year student pursuing Bachelors in engineering
> with majors in computer science from BITS Pilani Goa,India.
> I am interested to participate in gsoc 2013 and interested in Scaffold
> Hunter organization.
> My skill set includes C,Java,python,mysql and android application
> development.
> I am interested in the idea substructure search in the ideas list.
> If anyone could help me provide with the relative links for the further
> understanding of the idea and direct me with the requirements of the
> project?
> Thank you.
> 
> 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> 
> 
> 
> _______________________________________________
> Scaffoldhunter-users mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> 

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