Cytoscape Wiki
Cytoscape Users Meeting, Seattle April 25th
Agenda
- 9-9:10am Teachers introduce themselves, Iliana reviews agenda (max:10mins)
- 9:10-11:00am Cytoscape tutorial (1hr50mins, Iliana, Mike, Aditya, Allan)
- 11:00-12:15pm Three ISB scientists present their work using Cytoscape (1hr15mins in order: Jennifer Smith, Amy Schmid, Greg Carter ~25 mins each)
- 12:15-1pm Lunch (00:45, provided by the ISB)
- 1-2:30pm User-developer discussions (3 groups, 1:30hrs, 30mins for evolution game)
- 2:30pm-3pm Everyone meets in classroom, leader of each discussion group summarizes, adjourn
Tutorial
Download and unzip: http://db.systemsbiology.net/cytoscape/iavila/cytoscape2.2.zip
- The Basics Part I (Iliana, ~15mins)
- What is Cytoscape
Installing Cytoscape & running it (go to cytoscape.org download page, do not actually download!)
- Quick tour of Cytoscape (start Cytoscape, quick review of the Cytoscape Desktop)
- Network loading, network file formats (SIF, GML, major differences)
- Node naming in Cytoscape (as explained in Cytoscape manual)
- Network layout (quickly show it, do a layout)
- Navigation: selection of nodes and edges, zooming operations, network overview window, cyto-panels, etc.
- The Basics Part II (Allan,~15mins)
- Node attributes loading, node attributes file format, same for edge attributes
- Attributes browser
- Visual Sytles (explain, simple edit of an existing one, expression data section of tutorial will show students how to create a continuous calculator)
- Cytoscape Properties Dialog
- Filters and Editor (Allan, ~15mins)
- Expression Data (Aditya,~20mins)
- File format
- How to load the file, view it in attributes browser
- Visual style setting of node colors
- PValues
If time, mention available plugins for expression data, perhaps show DynamicExpression
- Gene Ontology (Mike,~15mins)
- Gene Ontology server wizard
- How to annotate genes in the network
- How to load your own annotations file for your species
- Plugin Overview (group,~25mins)
- Mike: How to load plugins
- Mike: Show plugins page on cytoscape.org and mention variety
Mike: BINGO, GraphMerge
Aditya: LitSearch
Iliana: BioNetBuilder, NetworkAnalyzer
Discussion Guide for User/Developer Discussions
For this section we will divide into 3 groups of ~13 students. Each group will have two moderators, one of which should take notes. The moderators are: Allan, Aditya, Annette, Mike, Iliana, and an ISB volunteer for taking notes, Susi.
The first 30 mins should be spent playing the evolution game that Ethan Cerami invented. The game goes like this:
- Give each person an index card. Instruct them to write the ONE thing they would like to add/change/fix about Cytoscape
- Make groups of 3, each group has to have a discussion to select one of the 3 index cards
- Moderator collects winning index card from each group. Tallies results on a board to get top winning card. Keep this card.
- When all discussion groups get back together in classroom at 2:30pm, there will be 3 winning index cards. Briefly discuss each, and do a vote to prioritize them (1st, 2nd, 3rd).
After the evolution game, the following list of discussion items can be shown/distributed to start a discussion for the next hour.
Following are topics of interest that we would like to cover in the user discussions. They can be used to prompt discussion if needed. Idea is to quickly show a list of topics at the beginning of the discussion session, then let the audience drive.
1. Installation experience.
2. Running Cytoscape
- running a command line script vs. double-clickig an icon
- how does Cytoscape play with other programs used on a regular basis?
3. User interface and usability. Are the GUI features intuitive?
- Do the menus make sense?
- Do you like cytopanels (i.e. frames within frames, or separate windows)?
- Is the relationship of the graph model to attribute data to visualization clear?
4. Visual Styles
- Is the mapping of network data to visual attributes easy?
- is the definition and use of filters easy?
5. Performance & responsiveness: Operations on large networks too slow?
6. Features: which are useful? useless?
- Are there any features that you do NOT use? If so why?
- Are there any features that you find confusing or particularly annoying?
7. Plugins: Are they easy to use?
- Do plugins work for you? Are they easy to use and integrate with cytoscape?
- What is the next plugin you would like to see someone write?
Conclusions
IlianaAvila April 26th, 2006
I think that the meeting went well. We had a chaotic start because students were having issues with connecting to the wireless network. Additionally, students were running OS X and Windows. The students that were running Windows had no problems to launch Cytoscape (just double click on the .bat script). But OS X students could not double click on cytoscape.sh to run Cytoscape. Some of them double clicked on cytoscape.jar, but the plugins did not get loaded. The instructors had to personally help them by opening a terminal and typing ./cytoscape.sh.
First lesson: we need to have an OS independent way of starting Cytoscape that loads plugins
Student's previous experience with Cytoscape varied from none to as much as 6 or more months of using it. Therefore, some of them thought the tutorial's pace was too fast, and others felt it was too slow. Additionally, the tutorial needs to be more seamless, and, more focused. Suggestions to improve the tutorial are:
- Some students don't know what Cytoscape is. We need to have a stronger introduction to biological networks and systems biology
- Start with a biological application and describe biological data that will be used (mRNA, proteomics, etc)
- Propose biological questions and show how Cytoscape and selected plugins can be used to answer them
- Instructors should rehearse tutorial
- Tutorial should be longer than 2 hours (maybe 2:30 would be good enough)
The ISB user's presentations of their research using Cytoscape were very well received. These talks helped students to tie together concepts we had taught during the tutorial, and showed them how to use them in practice. Also, the fact that the research projects were published gave users high confidence in the usefulness of Cytoscape. The speakers did a very good job of clearly stating how Cytoscape facilitated the process of creating biological hypothesis that would be hard to come by without using Cytoscape.
During lunch, I shared a table with 3 students, and learned more about them. Important things I remember about our conversation were:
- Two main reasons why they use Cytoscape, as opposed to competing software, are: it is for free, and, it allows users to load ANY type of data they want to use. Similar software (they mentioned Ariadne, Insightfull) is too expensive, too hard to load data, and low quality database contents.
- Cytoscape needs to have database connectivity and ID mapping services
- Cytoscape needs to support more model organisms
- Cellular localization needs to be visualized in some way
The discussion in my group was very productive. We played the evolution game, and there were two winning ideas:
- Make attributes multi-dimensional, kind of like metanodes, but for attributes
- Make UI more consistent and intuitive (context menus, operations that act on a group of selected nodes, bypassing visual mapper to set visual properties).
People seemed to be happy after we adjourned. It seems to me that Cytoscape has a great opportunity to grow and reach more people right now. I think we need to take advantage of this opportunity now by focusing some of our resources on this kind of outreach projects and trying to base our releases on some of the issues that are brought up by end-users.