scaffoldhunter-devel — Discussion list for Scaffold Hunter developers

[Scaffoldhunter-devel] New Bug/Feature Tracker State "on-hold"

[Till S. <til...@tu...>]

Dear SH developers, 
We have added a new tracker state "on-hold": 

* If a bug/feature has been partially fixed/implemented, but some kind of dependency prevents further work until the dependency is fulfilled, a bug should be marked as on-hold. The dependency may be another bug/feature or a general organization issue. 

See [1] for a complete list of tracker states. 

Regards,
Till

[1] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=tracker

-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] New Tracker States

[Till S. <til...@tu...>]

Hi, 
we have two new tracker states "re-opened" and "needs-merge":

re-opened: A bug/feature that was in a closed state or review-state, but needs to be re-opened because the bug/ was not fixed (correctly), the bug/feature implementation caused some side-effect or the feature was incomplete.
needs-merge: If a bug/feature in a feature branch has been fixed/implemented and is reviewed but cannot be merged immediately this state should indicate, that the associated code/work still needs to be merged. A typical example is a fix/feature, that breaks some backward compatibility and therefore needs to be hold back until the next major release.

For a full list of tracker states have a look at our wiki page [1]

Regards, 
Till

[1] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=tracker

-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

Re: [Scaffoldhunter-devel] export clustering results

[Till S. <til...@tu...>]

Hi, 
SH currently does not support an export of the clustering results yet. The clustering results are stored as serialized session data in an XML format and stored in a single database field (session_data.session_data). The results are therefore not so easy to extract from the database directly, but it should be possible to reconstruct them with an XML Parser. Alternatively, if you are just interested in the flat clustering (and not the hierarchy) you can create  and export a subset for each cluster by clicking the horizontal dendrogram bar of each clusters LCA (lowest common ancestor) to select the complete cluster/subtree at once (its might be a bit cumbersome for many clusters). If you are familiar with Java, you can also simply modify SH and create a custom export by grabbing the root node of the dendrogram, which is stored as an attribute of the dendrogram view.  The node class is called HierarchicalClusterNode. It simply has a left and right child  or contains a reference to the associated molecule, in the case of leaf nodes.

If you are interested in a functionality to automatically create subsets based on the partitioning implied by the cluster selection bar (the red bar which is draggable) or to export the complete hierarchy, please open a feature request at [1]. If you can elaborate your goal a bit deeper, we can also think about other workarounds.

Regards,
Till

[1] https://sourceforge.net/p/scaffoldhunter/feature-requests/?source=navbar

Am Donnerstag, 14. Juli 2016, 12:27:14 schrieb Gonzalo Colmenarejo:
> Hi,
> 
> how can I export the clustering results appearing in the SH? Or at least is
> it there in the database? If yes what would be the tables involved?
> 
> Thanks
> 
> Gonzalo
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] export clustering results

[Gonzalo C. <col...@gm...>]

Hi,

how can I export the clustering results appearing in the SH? Or at least is
it there in the database? If yes what would be the tables involved?

Thanks

Gonzalo

Re: [Scaffoldhunter-devel] How to run the system in Eclipse environment?

[Till S. <til...@tu...>]

Hi, 
the git repository contains an eclipse project that you can use directly and which configures all dependencies on libraries, etc. After you have imported that eclipse project into your workspace, you simply need to run the main method, which is located at edu.udo.scaffoldhunter.ScaffoldHunter.java. You may also want to modify your launch configuration, such that you use a little bit more ram  (e.g. add "-Xmx2G" for 2 GiB max heap space).

You may also want to read the manual.pdf to get a better knowledge about how to use the SH. It is contained in the SH-bundle (zip-file) you can download from the Website. 
We also have a small tutorial [1] an FAQ section [2] and a few developer documentations [3] along with our JavaDoc. 

Regards,
Till

[1] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=guides:start
[2] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=faq
[3] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=documentation:devel


Am Mittwoch, 28. Oktober 2015, 18:45:06 schrieb Wang, Dayu:
> --------------------------------------------------------------------------------------------------------------
> 
> Dear Madam/Sir,
> 
> Sorry to occupy your precious time.  We are graduate students in the University of Missroui-Kansas City (US).  We are very interest in the software Scaffold Hunter and already obtained the source code from SourceForge.  However, we have a hard time to try to run the system in the Eclipse environment.  Therefore, I am writing this letter to see if you can help us set up the system in order to let it run in Eclipse.  We selected Scaffold Hunter to complete our class project of software architecture and design.  We attempt to recover the architecture of the Scafflod Hunter system from the source code, using ArchStudio.
> Please let us be grateful if you would like to share the set up guide of the source code with us.  Any help/assistance/suggesions will be really appreciated.  Sorry to bother you again.  And we are looking forward to see you reply.
> 
> Sincerely,
> 
> Dayu Wang and Ran Chen
> 
> Department<mailto:day...@ma...> of Computer Science and Electrical Engineering
> University of Missouri-Kansas City
> U.S.
> 
> --------------------------------------------------------------------------------------------------------------
> Please add day...@ma...<mailto:day...@ma...> to your "Safe Senders" list to allow my emails to safely come into your inbox.
> 
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] How to run the system in Eclipse environment?

[Wang, D. (UMKC-Student) <day...@ma...>]

--------------------------------------------------------------------------------------------------------------

Dear Madam/Sir,

Sorry to occupy your precious time.  We are graduate students in the University of Missroui-Kansas City (US).  We are very interest in the software Scaffold Hunter and already obtained the source code from SourceForge.  However, we have a hard time to try to run the system in the Eclipse environment.  Therefore, I am writing this letter to see if you can help us set up the system in order to let it run in Eclipse.  We selected Scaffold Hunter to complete our class project of software architecture and design.  We attempt to recover the architecture of the Scafflod Hunter system from the source code, using ArchStudio.
Please let us be grateful if you would like to share the set up guide of the source code with us.  Any help/assistance/suggesions will be really appreciated.  Sorry to bother you again.  And we are looking forward to see you reply.

Sincerely,

Dayu Wang and Ran Chen

Department<mailto:day...@ma...> of Computer Science and Electrical Engineering
University of Missouri-Kansas City
U.S.

--------------------------------------------------------------------------------------------------------------
Please add day...@ma...<mailto:day...@ma...> to your "Safe Senders" list to allow my emails to safely come into your inbox.

Re: [Scaffoldhunter-devel] How to find the exact input molecules?

[Jing Lu <aj...@gm...>]

Thanks, Till and Shamshad,

Ctrl-M is very helpful and also the tooltip dialog. But, I need to wait for
a while for tooltip to show up. I also find the table view useful as I need
to find a particular molecule. Does Scaffold Hunter have function for
searching?


Best,
Jing

On Mon, Sep 28, 2015 at 5:56 AM, Till Schäfer <til...@tu...
> wrote:

> Dear Jing,
>
> As Shamshad already said, the Scaffold Tree View only displays scaffolds
> of the imported molecules, but you can toggle the display of the molecules
> which are assigned to the scaffold nodes. If you like to learn more about
> the chemical purpose of the scaffold tree you can read the publication [1].
> The molecules are shown directly in other views such as the heatmap, table,
> dendrogram and plot view.
>
>
>
> To keep track of your imported data, you have to do two steps:
>
> 1. Ensure that you import the ID as a property together with your
> molecules (see the manual.pdf file contained in the Scaffold Hunter zip
> bundle for further details)
>
> 2. Configure the Tool-Tip-Dialog to display them (Menu: Session ->
> Configure Tooltip) or use the table view
>
>
>
> The ID will be not displayed for scaffolds but for molecules, as the
> scaffolds are generated and not contained in the input data.
>
>
>
> If you are importing smiles data, Scaffold Hunter re-generates the smiles
> in order to calculate canonical smiles (to keep track of the molecules).
> This smiles might be different from your input data, as there may exist
> different correct smiles for a single molecule. If you want to keep your
> old smiles string, please import it as a property. You will then be able to
> see both, the canonical smiles generated from Scaffold Hunter and the
> original smiles from your imported data.
>
>
>
> @Shamshad: thx for explaining the scaffold tree
>
>
>
> Regards,
>
> Till
>
>
>
> [1] Interactive exploration of chemical space with Scaffold Hunter
> Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea,
> Petra Mutzel, Herbert Waldmann
> Nature Chemical Biology, 2009, 5, 581-583
>
>
>
> Am Samstag, 26. September 2015, 23:31:53 schrieb Shamshad Alam:
>
> > Hi Jing,
>
> >
>
> > I contributed to scaffold hunter a year ago and worked on some feature
>
> > requests.
>
> >
>
> > As far as I know scaffolds are generated by pruning terminal chains and
>
> > thereafter cycles. So SMILE string is likely to differ from original
>
> > molecules.
>
> >
>
> > >> How to keep track of the exact molecule?
>
> > Tree view only shows scaffolds by default. If you want to see molecules
>
> > too, press Ctrl + M, or in Tree menu check 'Show Scaffold Molecules'. I
>
> > guess it might help you.
>
> >
>
> > >> Does Scaffold Hunter convert the original input molecules to a
> scaffold
>
> > first?
>
> > It does when you generate scaffold tree.
>
> >
>
> > >> Because, when I was checking the leaf nodes, the structure does not
>
> > really exist in my input file. How to interpret that?
>
> > In scaffold view at the leaf node what you see may exist as a
> substructure
>
> > of one or more molecules.
>
> >
>
> > I hope it will help you and clear your some doubts. If you have any
> further
>
> > queries let us know.
>
> >
>
> >
>
> > Cheers,
>
> > Shamshad
>
> >
>
> > On Sat, Sep 26, 2015 at 9:29 PM, Jing Lu <aj...@gm...> wrote:
>
> >
>
> > > Dear Scaffold Hunter developers,
>
> > >
>
> > >
>
> > > Sorrry to send this again. But, I am not sure where to ask questions. I
>
> > > try to put ligand id to tooltip to keep track of each molecule. It
> seems
>
> > > like impossible. Moreover, I find Scaffold Hunter changes the SMILE
> string
>
> > > I put in the input file. How to keep track of the exact molecule?
>
> > >
>
> > > Does Scaffold Hunter convert the original input molecules to a scaffold
>
> > > first? Because, when I was checking the leaf nodes, the structure does
> not
>
> > > really exist in my input file. How to inteperate that?
>
> > >
>
> > >
>
> > >
>
> > > Thanks,
>
> > > Jing
>
> > >
>
> > >
>
> > >
> ------------------------------------------------------------------------------
>
> > >
>
> > > _______________________________________________
>
> > > Scaffoldhunter-devel mailing list
>
> > > Sca...@li...
>
> > > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
>
> > >
>
> > >
>
> >
>
> >
>
> >
>
> --
>
> Dipl.-Inf. Till Schäfer
>
> TU Dortmund University
>
> Chair 11 - Algorithm Engineering
>
> Otto-Hahn-Str. 14 / Room 237
>
> 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
>

Re: [Scaffoldhunter-devel] How to find the exact input molecules?

[Till S. <til...@tu...>]

Dear Jing, 
As Shamshad already said, the Scaffold Tree View only displays scaffolds of the imported molecules, but you can toggle the display of the molecules which are assigned to the scaffold nodes. If you like to learn more about the chemical purpose of the scaffold tree you can read the publication [1]. The molecules are shown directly in other views such as the heatmap, table, dendrogram and plot view. 

To keep track of your imported data, you have to do two steps: 
1. Ensure that you import the ID as a property together with your molecules (see the manual.pdf file contained in the Scaffold Hunter zip bundle for further details)
2. Configure the Tool-Tip-Dialog to display them (Menu: Session -> Configure Tooltip) or use the table view

The ID will be not displayed for scaffolds but for molecules, as the scaffolds are generated and not contained in the input data. 

If you are importing smiles data, Scaffold Hunter re-generates the smiles in order to calculate canonical smiles (to keep track of the molecules). This smiles might be different from your input data, as there may exist different correct smiles for a single molecule. If you want to keep your old smiles string, please import it as a property. You will then be able to see both, the canonical smiles generated from Scaffold Hunter and the original smiles from your imported data. 

@Shamshad: thx for explaining the scaffold tree

Regards,
Till

[1] *Interactive exploration of chemical space with Scaffold Hunter*


Am Samstag, 26. September 2015, 23:31:53 schrieb Shamshad Alam:
> Hi Jing,
> 
> I contributed to scaffold hunter a year ago and worked on some feature
> requests.
> 
> As far as I know scaffolds are generated by pruning terminal chains and
> thereafter cycles. So SMILE string is likely to differ from original
> molecules.
> 
> >>  How to keep track of the exact molecule?
> Tree view only shows scaffolds by default. If you want to see molecules
> too, press Ctrl + M, or in Tree menu check 'Show Scaffold Molecules'. I
> guess it might help you.
> 
> >> Does Scaffold Hunter convert the original input molecules to a scaffold
> first?
> It does when you generate scaffold tree.
> 
> >> Because, when I was checking the leaf nodes, the structure does not
> really exist in my input file. How to interpret that?
> In scaffold view at the leaf node what you see may exist as a substructure
> of one or more molecules.
> 
> I hope it will help you and clear your some doubts. If you have any further
> queries let us know.
> 
> 
> Cheers,
> Shamshad
> 
> On Sat, Sep 26, 2015 at 9:29 PM, Jing Lu <aj...@gm...> wrote:
> 
> > Dear Scaffold Hunter developers,
> >
> >
> > Sorrry to send this again. But, I am not sure where to ask questions. I
> > try to put ligand id to tooltip to keep track of each molecule. It seems
> > like impossible. Moreover, I find Scaffold Hunter changes the SMILE string
> > I put in the input file. How to keep track of the exact molecule?
> >
> > Does Scaffold Hunter convert the original input molecules to a scaffold
> > first? Because, when I was checking the leaf nodes, the structure does not
> > really exist in my input file. How to inteperate that?
> >
> >
> >
> > Thanks,
> > Jing
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Scaffoldhunter-devel mailing list
> > Sca...@li...
> > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> >
> >
> 
> 
> 
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

Re: [Scaffoldhunter-devel] How to find the exact input molecules?

[Shamshad A. <sha...@gm...>]

Hi Jing,

I contributed to scaffold hunter a year ago and worked on some feature
requests.

As far as I know scaffolds are generated by pruning terminal chains and
thereafter cycles. So SMILE string is likely to differ from original
molecules.

>>  How to keep track of the exact molecule?
Tree view only shows scaffolds by default. If you want to see molecules
too, press Ctrl + M, or in Tree menu check 'Show Scaffold Molecules'. I
guess it might help you.

>> Does Scaffold Hunter convert the original input molecules to a scaffold
first?
It does when you generate scaffold tree.

>> Because, when I was checking the leaf nodes, the structure does not
really exist in my input file. How to interpret that?
In scaffold view at the leaf node what you see may exist as a substructure
of one or more molecules.

I hope it will help you and clear your some doubts. If you have any further
queries let us know.


Cheers,
Shamshad

On Sat, Sep 26, 2015 at 9:29 PM, Jing Lu <aj...@gm...> wrote:

> Dear Scaffold Hunter developers,
>
>
> Sorrry to send this again. But, I am not sure where to ask questions. I
> try to put ligand id to tooltip to keep track of each molecule. It seems
> like impossible. Moreover, I find Scaffold Hunter changes the SMILE string
> I put in the input file. How to keep track of the exact molecule?
>
> Does Scaffold Hunter convert the original input molecules to a scaffold
> first? Because, when I was checking the leaf nodes, the structure does not
> really exist in my input file. How to inteperate that?
>
>
>
> Thanks,
> Jing
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Scaffoldhunter-devel mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
>
>


-- 

Shamshad Alam
+91 8800749256 | India
Twitter: @Saral_Shamshad
Google+: +ShamshadAlamNpti
LinkedIN: http://lnkd.in/b_EzeeN
FB: shamshad.saralindia <https://www.facebook.com/shamshad.saralindia>

[Scaffoldhunter-devel] How to find the exact input molecules?

[Jing Lu <aj...@gm...>]

Dear Scaffold Hunter developers,


Sorrry to send this again. But, I am not sure where to ask questions. I try
to put ligand id to tooltip to keep track of each molecule. It seems like
impossible. Moreover, I find Scaffold Hunter changes the SMILE string I put
in the input file. How to keep track of the exact molecule?

Does Scaffold Hunter convert the original input molecules to a scaffold
first? Because, when I was checking the leaf nodes, the structure does not
really exist in my input file. How to inteperate that?



Thanks,
Jing

[Scaffoldhunter-devel] Git Migration Completed

[Till S. <til...@tu...>]

Dear Developers, 
We have just finished the move of the Scaffold Hunter code repository [1]. Please note, that it only matches SVN revisions 102 upward, since there where some problems in the folder structure in lower revisions (trunk folder was not always present). Therefore we are loosing commits made during the development of version 1.x of Scaffold Hunter. All commits since the start of the development of version 2 are migrated over to Git. If you are a developer, you still have read-only access to the old SVN repository. It is now unavailable to the public. 

If you are committing to some of the branches other than "master", please take care you do not commit temporary files. We have not migrated the SVN ignore properties for this branches. 

If your Author name is not linked to your Sourceforge Profile, please make sure, you have added the e-mail address used in your commits to your Sourceforge profile. 

Again: If you experience any problems with the new git repository/branches, please contact us on this mailing list. I am happy to notice migration mistakes early (if there are some). 


Regards, 
Till 

[1] https://sourceforge.net/p/scaffoldhunter/git-code/ci/master/tree/


-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

Re: [Scaffoldhunter-devel] Migration to GIT

[Till S. <til...@tu...>]

Dear Developers of Scaffold Hunter, 
the migration of the code repository will be delayed until we have have collected missing informations about some authors. However, it will be done in the next days. 

Regards,
Till

Am Mittwoch, 26. August 2015, 15:53:41 schrieb Till Schäfer:
> Dear Developers of Scaffold Hunter, 
> we are currently migrating our VCS system from SVN to GIT. The move was considered for a longer time for various reasons, but especially the latest sourceforge data loss (we were affected by loosing some commits) motivated us to migrate now.
> 
> The new GIT repositories will be also hosted on sourceforge.  The old SVN repositories will we be made unavailable to the public and read only for developers. The history, branches and tags will be preserved. You (will) find the new git-urls for cloning / fetching / pushing here [1].
> 
> The switch is already completed for the web repository. The switch for the code repository will be made today in the evening (about 17:00 UTC / 19:00 German time) to not interfere with work in progress. 
> 
> If you have some uncommitted changes (after the switch), you will have to clone the new git repositories and manually apply your changes to them.
> 
> If you have any problems with the new git repositories, please let us know. 
> 
> Regards,
> Till
> 
> [1] https://sourceforge.net/p/scaffoldhunter/_list/git
> 
> 
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] Migration to GIT

[Till S. <til...@tu...>]

Dear Developers of Scaffold Hunter, 
we are currently migrating our VCS system from SVN to GIT. The move was considered for a longer time for various reasons, but especially the latest sourceforge data loss (we were affected by loosing some commits) motivated us to migrate now.

The new GIT repositories will be also hosted on sourceforge.  The old SVN repositories will we be made unavailable to the public and read only for developers. The history, branches and tags will be preserved. You (will) find the new git-urls for cloning / fetching / pushing here [1].

The switch is already completed for the web repository. The switch for the code repository will be made today in the evening (about 17:00 UTC / 19:00 German time) to not interfere with work in progress. 

If you have some uncommitted changes (after the switch), you will have to clone the new git repositories and manually apply your changes to them.

If you have any problems with the new git repositories, please let us know. 

Regards,
Till

[1] https://sourceforge.net/p/scaffoldhunter/_list/git

-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

Re: [Scaffoldhunter-devel] Want to Contribute To your Project

[Till S. <til...@tu...>]

Hi, 
we are using a subversion repository at sourceforge [1]. You should use the included eclipse project. 

Please use the devel mailinglist for further communication. 

Regards, 
Till

[1] http://sourceforge.net/p/scaffoldhunter/code/HEAD/tree/

Am Montag, 19. Januar 2015, 20:39:48 schrieb Abhishek Nagpal:
> Hello,
> 
> I am sorry, but I am new to this and I could not find the link to download
> your code. Can you please share a link.
> 
> Thank You
> Abhishek
> 
> On Mon, Jan 19, 2015 at 6:04 PM, Till Schäfer <til...@tu...
> > wrote:
> 
> > Hi,
> > you can try to implement Feature Request 16 [1]. Please provide patched
> > directly to the devel mailinglist, so we can discuss them there.
> >
> > Regards,
> > Till
> >
> > [1] http://sourceforge.net/p/scaffoldhunter/feature-requests/16/
> >
> > Am Montag, 19. Januar 2015, 17:42:30 schrieb Abhishek Nagpal:
> > > Hello,
> > >
> > > Thank You for informing about GSOC. But I want to do some coding and
> > learn
> > > about open source. So if you could give me some task that I could start
> > > with, will help a lot.
> > >
> > > Thank You
> > > Abhishek
> > >
> > > On Mon, Jan 19, 2015 at 4:46 PM, Till Schäfer <
> > til...@tu...
> > > > wrote:
> > >
> > > > Hi,
> > > > just to make this clear: we are not sure yet, if we will participate at
> > > > GSOC this year.
> > > >
> > > > If you just want to do some coding anyway, feel free to contact us
> > again.
> > > > We will then find some tasks for you.
> > > >
> > > > Regards,
> > > > Till
> > > >
> > > > Am Sonntag, 18. Januar 2015, 19:05:11 schrieb Abhishek Nagpal:
> > > > > Hello,
> > > > >
> > > > > I am Abhishek Nagpal ,an undergraduate from BITS PILANI  ,currently
> > > > > pursuing my Msc(Tech) Information Systems.I would like to be
> > contributor
> > > > to
> > > > > scaffoldhunter.Is there a way I could contribute to it or any other
> > > > > bugs that can be fixed to help me get started.I am a beginner in open
> > > > > source. So in any way that I could help to get me started will be
> > > > > helpful.
> > > > >
> > > > > Thank You
> > > > >
> > > > > Abhishek Nagpal
> > > > --
> > > > Dipl.-Inf. Till Schäfer
> > > > TU Dortmund University
> > > > Chair 11 - Algorithm Engineering
> > > > Otto-Hahn-Str. 14 / Room 237
> > > > 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
> > > >
> > --
> > Dipl.-Inf. Till Schäfer
> > TU Dortmund University
> > Chair 11 - Algorithm Engineering
> > Otto-Hahn-Str. 14 / Room 237
> > 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
> >
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] Fwd: Re: Want to Contribute To your Project

[Till S. <til...@tu...>]

Viele Grüße 
Till

----------  Weitergeleitete Nachricht  ----------

Betreff: Re: [Scaffoldhunter-devel] Want to Contribute To your Project
Datum: Montag, 19. Januar 2015, 13:34:17
Von: Till Schäfer <til...@tu...>
An: Abhishek Nagpal <abh...@gm...>

Hi, 
you can try to implement Feature Request 16 [1]. Please provide patched directly to the devel mailinglist, so we can discuss them there. 

Regards, 
Till

[1] http://sourceforge.net/p/scaffoldhunter/feature-requests/16/

Am Montag, 19. Januar 2015, 17:42:30 schrieb Abhishek Nagpal:
> Hello,
> 
> Thank You for informing about GSOC. But I want to do some coding and learn
> about open source. So if you could give me some task that I could start
> with, will help a lot.
> 
> Thank You
> Abhishek
> 
> On Mon, Jan 19, 2015 at 4:46 PM, Till Schäfer <til...@tu...
> > wrote:
> 
> > Hi,
> > just to make this clear: we are not sure yet, if we will participate at
> > GSOC this year.
> >
> > If you just want to do some coding anyway, feel free to contact us again.
> > We will then find some tasks for you.
> >
> > Regards,
> > Till
> >
> > Am Sonntag, 18. Januar 2015, 19:05:11 schrieb Abhishek Nagpal:
> > > Hello,
> > >
> > > I am Abhishek Nagpal ,an undergraduate from BITS PILANI  ,currently
> > > pursuing my Msc(Tech) Information Systems.I would like to be contributor
> > to
> > > scaffoldhunter.Is there a way I could contribute to it or any other
> > > bugs that can be fixed to help me get started.I am a beginner in open
> > > source. So in any way that I could help to get me started will be
> > > helpful.
> > >
> > > Thank You
> > >
> > > Abhishek Nagpal
> > --
> > Dipl.-Inf. Till Schäfer
> > TU Dortmund University
> > Chair 11 - Algorithm Engineering
> > Otto-Hahn-Str. 14 / Room 237
> > 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
> >
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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
-------------------------------------------------------------
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

Re: [Scaffoldhunter-devel] Want to Contribute To your Project

[Till S. <til...@tu...>]

Hi,
just to make this clear: we are not sure yet, if we will participate at GSOC this year. 

If you just want to do some coding anyway, feel free to contact us again. We will then find some tasks for you. 

Regards,
Till

Am Sonntag, 18. Januar 2015, 19:05:11 schrieb Abhishek Nagpal:
> Hello,
> 
> I am Abhishek Nagpal ,an undergraduate from BITS PILANI  ,currently
> pursuing my Msc(Tech) Information Systems.I would like to be contributor to
> scaffoldhunter.Is there a way I could contribute to it or any other
> bugs that can be fixed to help me get started.I am a beginner in open
> source. So in any way that I could help to get me started will be
> helpful.
> 
> Thank You
> 
> Abhishek Nagpal
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

Re: [Scaffoldhunter-devel] GSOC 2015

[Till S. <til...@tu...>]

Hi,
you can try to implement feature request 13 [1]. Please send patches to the devel mailinglist.  

Regards, 
Till

Am Donnerstag, 15. Januar 2015, 23:19:52 schrieb navya sri nizamkari:
> Hi,
> 
> I would like to code.Can you help me by providing some tasks?
> 
> Thanks.
> 
> On Thu, Jan 15, 2015 at 4:01 PM, Till Schäfer <til...@tu...
> > wrote:
> 
> > Hi,
> > we are not sure yet, if we will participate this year. Therefore, i cannot
> > say anything about GSOC at this time. If you just want to do some coding
> > anyway, feel free to contact us again. We will then find some tasks for you.
> >
> > Regards,
> > Till
> >
> > Am Mittwoch, 14. Januar 2015, 20:51:56 schrieb navya sri nizamkari:
> > > Hello,
> > >
> > > I am Navya Sri ,an undergraduate from BITS PILANI hyderabad ,currently
> > > pursuing my B.E Hons in Computer Science.I would like to be contributor
> > to
> > > scaffoldhunter and do my GSOC this year through it.I really liked the
> > > project on subgraph network from last year.Is there a way I could
> > > contribute to it or any other bugs that can be fixed to help me get
> > started
> > > ?
> > >
> > > Thank You
> > --
> > Dipl.-Inf. Till Schäfer
> > TU Dortmund University
> > Chair 11 - Algorithm Engineering
> > Otto-Hahn-Str. 14 / Room 237
> > 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
> >
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] Want to Contribute To your Project

[Abhishek N. <abh...@gm...>]

Hello,

I am Abhishek Nagpal ,an undergraduate from BITS PILANI  ,currently
pursuing my Msc(Tech) Information Systems.I would like to be contributor to
scaffoldhunter.Is there a way I could contribute to it or any other
bugs that can be fixed to help me get started.I am a beginner in open
source. So in any way that I could help to get me started will be
helpful.

Thank You

Abhishek Nagpal

Re: [Scaffoldhunter-devel] GSOC 2015

[Till S. <til...@tu...>]

Hi, 
we are not sure yet, if we will participate this year. Therefore, i cannot say anything about GSOC at this time. If you just want to do some coding anyway, feel free to contact us again. We will then find some tasks for you. 

Regards,
Till

Am Mittwoch, 14. Januar 2015, 20:51:56 schrieb navya sri nizamkari:
> Hello,
> 
> I am Navya Sri ,an undergraduate from BITS PILANI hyderabad ,currently
> pursuing my B.E Hons in Computer Science.I would like to be contributor to
> scaffoldhunter and do my GSOC this year through it.I really liked the
> project on subgraph network from last year.Is there a way I could
> contribute to it or any other bugs that can be fixed to help me get started
> ?
> 
> Thank You
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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

[Scaffoldhunter-devel] GSOC 2015

[navya s. n. <nav...@gm...>]

Hello,

I am Navya Sri ,an undergraduate from BITS PILANI hyderabad ,currently
pursuing my B.E Hons in Computer Science.I would like to be contributor to
scaffoldhunter and do my GSOC this year through it.I really liked the
project on subgraph network from last year.Is there a way I could
contribute to it or any other bugs that can be fixed to help me get started
?

Thank You

[Scaffoldhunter-devel] Scaffold Hunter v2.4.1 released

[Till S. <til...@us...>]

A hotfix release for Scaffold Hunter has been published today. It fixes a bug, which causes the new heat map view to use 100% of one CPU core, whenever the view is active. Furthermore, this release enhances the heat map view with small workflow changes, such as an automatic sizing of the dendrogram, property and heat map part.

For more detailed information see the changelog [1] or the SVN history [2]. You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.4.1/

[1] http://sourceforge.net/projects/scaffoldhunter/files/2.4.1/changelog.txt/download
[2] https://sourceforge.net/p/scaffoldhunter/code/2810/log/

[Scaffoldhunter-devel] Scaffold Hunter v2.4.0 released

[Till S. <til...@us...>]

Scaffold Hunter v2.4.0 has been published today. This release adds a new heat map view [1] and includes many design, work flow, and stability improvements. Starting with this release, we officially support MariaDB as a MySQL alternative. 

The heat map view [1] displays hierarchical clustering results in a new way. It visualizes the property values by colors in a 2D matrix of molecules vs. properties. Similar molecules and similar properties are grouped together with the help of clustering, such that molecular similarities which are correlated to property similarities can be easily identified by visual inspection. The heat map view was developed during the Google Summer of Code 2014 by Werner Sturm.

Please note that the current release breaks session compatibility and that sessions from previous versions might not be fully restored.
For a more detailed explanation of the changes made in this version see the changelog [2] or the SVN history [3].
You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.4.0/

[1] https://a.fsdn.com/con/app/proj/scaffoldhunter/screenshots/heatmap.png
[2] https://sourceforge.net/projects/scaffoldhunter/files/2.4.0/changelog.txt/download
[3] https://sourceforge.net/p/scaffoldhunter/code/2787/log/?path=

Re: [Scaffoldhunter-devel] Improving Molecule Cloud

[<nl...@us...>]

Hi Andrew,

thank you very much for being willing to improve your code and to answer 
questions on layout implementation. We plan to release a new version of 
Scaffold Hunter without the Molecule Cloud view soon and will then try to add 
more efficient layout algorithms before your code is merged back into trunk. 
Please let us know when the refactoring is done.


Regards,
  Nils


On Wednesday 24 September 2014 22:58:27 Anjenson wrote:
> Hi everyone!
> 
> I am very sorry for being silent for such a long time. It's really tough
> time here as I got on the research project, that is referred to
> bioinformatics by the way.
> 
> But back to the deal, I have spent some time thinking about what can be
> changed in Molecule Cloud architecture in order to make it more
> intuitive. The only my idea is to integrate both StaticLayout and
> ForceLayout into Layout class. The reason is that the only differences
> between classes are
> 
>   *   the use of task queues when using StaticLayout and
>   * grouping when using ForceLayout.
> 
> I think that, first of all, we shouldn't create the difference in
> functionality and, secodly, I think that there may be situations when
> force layouts may benefit from task queues.
> 
> Also in order not to make any one of you, who would like to implement
> new layout, wait while I finish this I just want to say that the
> implementation of new layout algorithms is completely independent from
> the part I intend to refactor. There are some guidelines in the manual
> and, please, fill free to ask me directly I will try to be as responsive
> as possible.
> Just one more notice: it should be a preferred style to extend
> CloudLayouter.
> 
> With best regards,
>      Andrew "Anjenson" Zhilka

[Scaffoldhunter-devel] Improving Molecule Cloud

[Anjenson <hot...@gm...>]

Hi everyone!

I am very sorry for being silent for such a long time. It's really tough 
time here as I got on the research project, that is referred to 
bioinformatics by the way.

But back to the deal, I have spent some time thinking about what can be 
changed in Molecule Cloud architecture in order to make it more 
intuitive. The only my idea is to integrate both StaticLayout and 
ForceLayout into Layout class. The reason is that the only differences 
between classes are

  *   the use of task queues when using StaticLayout and
  * grouping when using ForceLayout.

I think that, first of all, we shouldn't create the difference in 
functionality and, secodly, I think that there may be situations when 
force layouts may benefit from task queues.

Also in order not to make any one of you, who would like to implement 
new layout, wait while I finish this I just want to say that the 
implementation of new layout algorithms is completely independent from 
the part I intend to refactor. There are some guidelines in the manual 
and, please, fill free to ask me directly I will try to be as responsive 
as possible.
Just one more notice: it should be a preferred style to extend 
CloudLayouter.

With best regards,
     Andrew "Anjenson" Zhilka

[Scaffoldhunter-devel] Bug Dependencies

[Till S. <til...@tu...>]

Hi, 
i have to report one more small change to the bug tracker. I have created two fields called "Depends On" and "Blocks". They are introduced to handle inter bug dependencies. 

-> blocks: This is a list of bug / feature request ids. This bug / feature request must be fixed / implemented before any of the listed blocked bugs can be fixed / implemented.
-> depends on: This is a list of bug / feature request ids. This bug / feature request depends of the fix / implementation of another bug and can only be completed afterwards.

Usually, a block entry “B” in a bug / feature request A implies a “depends on” entry “A” in bug / feature request B. Please ensure, that the dependency is always listed in both bugs (A and B). 

Sadly Allura does not allow to reference other bugs directly, so we must manually type the bug ids in a text field. 

For more informations about the bug tracker you can also have a look at the corresponding wiki [1].

Regards,
Till

[1] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=tracker

-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
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