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{*} This RFC is now officially closed, as Quick Find is now part of Cytoscape 2.4. I am however, keeping track of new feature requests below. === Cytoscape 2.5 Feature Requests === * From Kei: I demonstrated your Quick Find plugin today to our lab members. They are very impressed by the interactive filtering by numerical values. I got one suggestion for the feature. When user filters nodes with numerical values, the boundary values are shown as a popup (tooltip?), and it will disappear after user stop clicking on the range select slider. Is it possible to display boundary values always on the both sides of slider? |
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| For reference, here is the current Cytoscape toolbar: |
For reference, here is the '''current Cytoscape toolbar''': |
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| Here is the proposed tool bar with the Ximiam Open Office Icons: |
And, here is the '''proposed tool bar''' with the Ximiam Open Office Icons: attachment:proposed_tool_bar.png A few things to note: * I removed the hide/show actions (there seemed to be recent consensus that these were very confusing to end-users). These actions will, however continue to be available via the main Cytoscape menu. * I added a help button. * I added the Quick Find toolbar. |
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BennoSchwikowski, 07/20/2006 - Bravo! Love the new icons, Ethan. --Benno MikeSmoot, 07/20/2006 - I think the new icons look fine and would be happy to have our current ones replaced. I am, however, a little biased against bitmap graphics used for icons. A quick search for "Java SVG icons" turned up this link: http://forums.java.net/jive/thread.jspa?threadID=7504&start=0&tstart=0 which I thought was pretty interesting. It might be worth paying someone to create the few missing icons we'd need for Tango and donate them to the project. Scooter might have some ideas on SVG as well since I know he is pretty involved with that in Mozilla. Trey Ideker 7/21/2006 - Looking good. The one nice thing about the old icons is they were very colorful. Would you be willing to add back in some color (or at least see what it looks like). Also, while you are at it there must be many other functions accessible through the menu systems which should also be on the toolbar (e.g., import network). All icons available are listed [http://chianti.ucsd.edu/mes/cyto-icons/ here] |
About this document
This is an official Request for Comment (RFC) for a a new icon set in Cytoscape 2.4.
For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]
Status
This RFC is now officially closed, as Quick Find is now part of Cytoscape 2.4. I am however, keeping track of new feature requests below.
Cytoscape 2.5 Feature Requests
- From Kei: I demonstrated your Quick Find plugin today to our lab members. They are very impressed by the interactive filtering by numerical values. I got one suggestion for the feature. When user filters nodes with numerical values, the boundary values are shown as a popup (tooltip?), and it will disappear after user stop clicking on the range select slider. Is it possible to display boundary values always on the both sides of slider?
How to Comment
To view/add comments, please scroll down to the bottom of the page. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment.
Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.
Proposal
I'd like to propose that Cytoscape 2.4 adopt a new, more intuitive set of icons for the main tool bar. The current set of icons is not very intuitive, and a number of users find them very confusing.
As part of this RFC, I have explored a number of icon options:
[http://www.kde-look.org/index.php?xcontentmode=22x27 Linux KDE Icons]: Lots of beautiful icons, but unfortunately, none of the icon sets support key Cytoscape actions, e.g. zoom selected region.
[http://www.gnome-look.org/index.php?xcontentmode=120&PHPSESSID=9ca47374357d9e9552e40100e3f5da69 Linux Gnome Icons]: Same problem as the KDE icons. Lots of beautiful icons, but unfortunately, none of the icon sets support key Cytoscape actions, e.g. zoom selected region.
[http://www.codehaus.org/~bwalding/eclipse-icons Eclipe icons]: Has lots of potential, but I couldn't find all the corresponding zoom icons.
Stock icons from commercial companies. I found a number of relatively cheap icon sets for sale. These range in price from $100-$400. However, many of these icons have redistribution requirements. For example, icons can only be distributed as part of a binary or exe. For an example commercial set of icons, see: [http://glyphlab.com/stock_icons/index.html Glyph Lab].
- Custom icon design from a commercial company. I requested a quote from one icon design company to get an idea of how much custom icon design costs. Their quote was $60-$120 / icon.
[http://tango.freedesktop.org/Tango_Desktop_Project Tango Project]: This seemed to be the most promising option. From the web site, "The Tango Desktop Project exists to help create a consistent graphical user interface experience for free and Open Source software." Sounds very promising, and they have a great set of base icons. But, it is not yet finished, and there are lots of missing icons. Once Tango creates a complete set, I think we should re-evaluate.
After evaluating the above options, I stumbled upon the Open Office Icon set. More specifically, the [http://www.novell.com/coolsolutions/feature/1637.html Ximiam-themed Open Office Icon set].
I'd like to propose that we adopt this icon set for Cytoscape 2.4. Here are the major reasons for doing so:
Consistent and familiar visual metaphors. For example, the "save" icon looks like a disk, the "zoom in" icon looks like a magnifying glass with a +. All of these visual metaphors make sense and are very familiar.
Professionally designed. They just look good.
With over 1,000 icons, we have plenty to choose from. I was able to find good icons for all the Cytoscape actions in the tool bar, e.g. zoom selected, viz mapper, filter, etc. This is really important for future evolution as well, as we are not stuck with a small, limited set of icon options.
All icons are available in two sizes: 16x16 and 24x24.
This specific icon set is available under the LGPL. From the web site: "If you're putting together an application, you are free to use every one of these icons. Ximian has released the icons under the LGPL. This means that you can use the icons in your program free of charge. If you want to fork the icons into your own icon collection, you need to retain the license and the original copyrights, but from there you're free to do what you want."
For reference, here is the current Cytoscape toolbar:
attachment:existing_tool_bar.png
And, here is the proposed tool bar with the Ximiam Open Office Icons:
attachment:proposed_tool_bar.png
A few things to note:
- I removed the hide/show actions (there seemed to be recent consensus that these were very confusing to end-users). These actions will, however continue to be available via the main Cytoscape menu.
- I added a help button.
- I added the Quick Find toolbar.
Deferred Items
None defined yet.
Open Issues
None defined yet.
Comments
EthanCerami, 07/19/2006 - Sample comment to get things started... Love the new icons! Blah, blah, blah...
BennoSchwikowski, 07/20/2006 - Bravo! Love the new icons, Ethan. --Benno
MikeSmoot, 07/20/2006 - I think the new icons look fine and would be happy to have our current ones replaced. I am, however, a little biased against bitmap graphics used for icons. A quick search for "Java SVG icons" turned up this link: http://forums.java.net/jive/thread.jspa?threadID=7504&start=0&tstart=0 which I thought was pretty interesting. It might be worth paying someone to create the few missing icons we'd need for Tango and donate them to the project. Scooter might have some ideas on SVG as well since I know he is pretty involved with that in Mozilla.
Trey Ideker 7/21/2006 - Looking good. The one nice thing about the old icons is they were very colorful. Would you be willing to add back in some color (or at least see what it looks like). Also, while you are at it there must be many other functions accessible through the menu systems which should also be on the toolbar (e.g., import network).
All icons available are listed [http://chianti.ucsd.edu/mes/cyto-icons/ here]