About OpenBiomind-GUI

[Murilo Saraiva de Queiroz]

Hi Bhavesh,

First of all I would like to say that your code is very clean and well-organized. Keep up the good work! 

A few observations:

- executables in Linux and Mac OS X normally don't have extensions. The FileNameFilter used to set graphviz dot executable uses the expression dot.* so it doesn't accept the default /usr/bin/dot . Changing the expression to dot* solves the problem.

- There are a few Workspace-related preferences that don't make sense (Build automatically, Build order, referenced projects, etc.)

- Later we'll have to improve the task icons; perhaps we could using free icons from, for example, http://www.famfamfam.com/lab/icons/silk/ or http://www.freeiconsdownload.com . This is desirable but it's low priority.

- We'll have to add the required license information (see my other email about this)

- We need at least a README explaining that Java 6 is required (when running with Java 5 the application crashes), where pipeline.properties and openbiomind.jar can be found,  relevant web and email addresses, etc. 

- A tutorial and screencast would be particularly useful. The tutorial could be an edited, shorter version (text and images) of the screencast. I don't think a voice-over / narration is essential in the screencast; if it's taking too much time you can use pure text.

- One idea is to create a openbiomind-gui-examples package, containing the tutorial / screencast, small datasets to be used as examples, and pre-computed results to be visualized with the GUI. I think Lúcio can help you with those.

Thanks a lot!

Murilo Q.

--

Murilo Saraiva de Queiroz, MSc.
Senior Software Engineer  
http://www.vettalabs.com
http://www.tecnologiainteligente.com.br

[Bhavesh Sanghvi]

Hi Murilo,

 

Thank you for your feedback and appreciation. Here are my comments to the observations:

1.       Dot: I’ll update the code to accept dot*. However, the bin folder contain few more dot* files (dot2gxl and dotty), so I’ll add an error (I’ve few different things in mind, will notify once I look at those).

2.       Workspace related preference: Yes, they look bad. But until now, I’ve not found a clean way to remove them (someone once mentioned in the newsgroup that it can be done by editing the plugin.xml for the includes plug-ins, but that is not a maintainable way, as if the plug-in is updated, the process will need to be redone; moreover, it is not guaranteed to work correctly). Those options are coming due to the plug-in dependence (e.g. the navigator and file editor). Please let me know if someone knows how to remove them cleanly.

3.       Icons: Actually, I spent some time on icons; but I was not able to come with good icons for these tasks (I created the ones that are currently being use, and it is evident that I am not too good in drawing). Can we have more suggestions about which icon may be suitable for which task.

4.       License: Yes, I looked at that e-mail. Please send me the header text that I must paste at the top of each file (I looked at the link, but I am waiting for other responses on the other e-mail). Must I go ahead and change the license to LGPL?

5.       ReadMe, Screencast, Tutorial: I’ll be working on these in that order. I’ll put the readme and tutorial in wiki (may use GoogleDoc for creating PDF at the end for tutorial). Is there any free tool that converts from Google Code Wiki to PDF?

6.       Examples  package: I’ll try to create that. One option is to create a workspace with examples and check that in.

 

--

Thanks,

Bhavesh Sanghvi

[Murilo Saraiva de Queiroz]

On Mon, Aug 11, 2008 at 6:15 PM, Bhavesh Sanghvi <bsan...@cs.iastate.edu> wrote:

Thank you for your feedback and appreciation. Here are my comments to the observations:

1.       Dot: I'll update the code to accept dot*. However, the bin folder contain few more dot* files (dot2gxl and dotty), so I'll add an error (I've few different things in mind, will notify once I look at those).

One idea is to call dot -V and look for the words dot / Graphviz in the output...

2.       Workspace related preference: Yes, they look bad. But until now, I've not found a clean way to remove them (someone once mentioned in the newsgroup that it can be done by editing the plugin.xml for the includes plug-ins, but that is not a maintainable way, as if the plug-in is updated, the process will need to be redone; moreover, it is not guaranteed to work correctly). Those options are coming due to the plug-in dependence (e.g. the navigator and file editor). Please let me know if someone knows how to remove them cleanly.

I'll see if I can find something.
 

3.       Icons: Actually, I spent some time on icons; but I was not able to come with good icons for these tasks (I created the ones that are currently being use, and it is evident that I am not too good in drawing). Can we have more suggestions about which icon may be suitable for which task.

 Don't worry with the icons, as I said before they're low priority and eventually we can get someone to improve them.

4.       License: Yes, I looked at that e-mail. Please send me the header text that I must paste at the top of each file (I looked at the link, but I am waiting for other responses on the other e-mail). Must I go ahead and change the license to LGPL?

Let's wait a little for answers to that email, before doing any changes.
 

5.       ReadMe, Screencast, Tutorial: I'll be working on these in that order. I'll put the readme and tutorial in wiki (may use GoogleDoc for creating PDF at the end for tutorial). Is there any free tool that converts from Google Code Wiki to PDF?

I don't know. I don't like PDF very much, maybe if we just export to HTML  it would be OK...

6.       Examples  package: I'll try to create that. One option is to create a workspace with examples and check that in.

Yes, that's the idea.

Best,

[Murilo Saraiva de Queiroz]

Another observation I forgot to mention: the executable file of the Linux build is being named "eclipse". You can rename it to openbiomind or something like that editing the .product file. I don't know if the problem occurs in other builds.

Regarding your question: of course, your help with future maintenance is  very welcome! You did an excellent job this summer, and as new features are implemented in openbiomind the GUI will need to be updated (and we'll always need occasional bug fixes).  BTW, I think you should include a list of suggestions for future work in the README.

Best,

[Bhavesh Sanghvi]

I’ll do dot –V and the HTML documents.

 

--

Thanks,

Bhavesh Sanghvi

[Bhavesh Sanghvi]

In the beginning I tried to edit the name of the executable, but then I did not spend enough time on this (one option is to rename the file and zip it again). I’ll look in the .product file and update the name.

I’ll put a list of suggestions too.

 

--

Thanks,

Bhavesh Sanghvi

 

From: Murilo Saraiva de Queiroz [mailto:mur...@gmail.com]
Sent: Tuesday, August 12, 2008 8:54 AM
To: Bhavesh Sanghvi; Lúcio de Souza Coelho; openb...@googlegroups.com
Subject: Re: About OpenBiomind-GUI

 

Another observation I forgot to mention: the executable file of the Linux build is being named "eclipse". You can rename it to openbiomind or something like that editing the .product file. I don't know if the problem occurs in other builds.

[Bhavesh Sanghvi]

Hi Murilo,

 

To solve the dot issue on platforms where executable files need not have an extension, I updated the file dialog to allow files of the type “dot” as well as “dot.*”. Further to be extra sure, I updated the code to execute this file and check if the first line of the returned output starts with “dot – Graphviz” or not? In case, it does the file is accepted as valid dot utility. The changes are available in r57 (http://code.google.com/p/openbiomind-gui/source/detail?r=57).

 

--

Thanks,

Bhavesh Sanghvi