Two librarians at the University of Michigan have provided instruction on a network visualization tool called Cytoscape <www.cytoscape.org
> since 2009. Cytoscape is an open source software tool used to visualize and analyze biological networks and pathways. The Cytoscape core software is developed by a consortium but has a plug-in architecture that allows anyone to develop components that meet their specific needs. Plug-ins provide additional functionality to Cytoscape, such as importing data from specific external databases, determining portions of the network that cluster together, finding the shortest path between two nodes, and more. Plug-ins can be developed by anyone with programming knowledge, using the Cytoscape Java code library. The librarians have focused on Cytoscape because University of Michigan researchers have developed plug-ins for it, and it is freely available for anyone to use regardless of their affiliation. Cytoscape can be used to create any type of network including social and physical networks, although the University of Michigan librarians have focused on gene and protein interaction networks. The two librarians teaching Cytoscape both have a biological sciences education, one with an undergraduate degree and the other with a master's degree. The librarians have developed and delivered different types of instructional sessions for Cytoscape over the course of several years.
The librarians saw the opportunity for teaching classes on network visualization software to help fill researchers' burgeoning need to find patterns in large data sets. As noted above, unlike certain subscription resources, finding training courses on these types of resources can be challenging. Cytoscape's website has several tutorials [5
] in addition to a user manual [6
], but these do not have the advantages of an in-person training session, where participants can have their questions answered immediately and engage in collaborative learning. The librarians, therefore, developed a hands-on workshop for people to attend.
Stage 1: initial development
The first librarian-led Cytoscape training session using originally developed materials was offered at the University of Michigan in July 2009. To make the training more valuable to biomedical researchers, the tool was taught in a valid biological context. A biological case was presented and used throughout the instructional session in order to demonstrate Cytoscape functionality. Further course development led the librarians to a late 2009 article, summarizing two articles discussing three genes newly implicated in late onset Alzheimer's disease [7
]. These three genes—CLU, PICALM, and CR1—became the focus for the Cytoscape workshop. These novel gene associations for a well-researched inherited disease presented an interesting biological case study that allowed attendees of the training session to further investigate the new relationships between these genes that were previously considered unrelated.
The initial workshops covered the core features of Cytoscape, such as how to select nodes and edges or change visualization layouts (hierarchical, circular, etc.), and introduced several plug-ins: Michigan Molecular Interactions (MiMI), Enhanced Search, Shortest Path, and MCODE. The functionality of these plug-ins ranged from importing gene interaction data to isolating clusters of highly interconnected regions within a network (Table 1, online only). These plug-ins were chosen because they met at least one of the following criteria: were developed at the University of Michigan, had quality documentation available, or were frequently downloaded.
Stage 2: integrating changes
As course feedback was received, three more plug-ins were integrated into the Cytoscape workshop: MetScape, BINGO, and Agilent Literature Search (Table 1, online only). The addition of these plug-ins expanded on the type of data covered in the workshop. For example, the MetScape plug-in focuses on small molecules and compounds, in addition to genes. Adding these plug-ins required extending the training session period to two hours from one and a half. Presenting a longer training session did not seem to deter researchers from attending. Registration was full for the first two–hour long session, held in February 2011, for the classroom size of twenty-three people, with a wait list of ten ().
Figure 2 2 Timeline showing Cytoscape workshop highlights
Because of attendees' interest in using their own data, a new handout was provided at the extended workshop that illustrated how to import data into Cytoscape. The librarians determined that demonstrating how to import researchers' own data during the training was too time consuming. As a result, a handout walking users through importing network and attribute data was developed and distributed to session attendees. Thus, attendees could still get the necessary information for importing their data, but additional workshop time did not have to be designated to the task.
Stage 3: remote Cytoscape session
As the hands-on training sessions became more popular, the librarians realized they were being constrained by the physical training space. The training room only had twenty-three computers and was geographically located in a room that was difficult for registrants to find. Although hands-on training sessions are often preferred, there are many reasons why people are unable to attend them, such as having insufficient funds to travel to the training location or having time constraints. A remote training session is one solution to allow people to receive meaningful instruction. Blyth et al. found that the amount of money and time saved for many participants of the online faculty development workshops that they offered made this form of training worthwhile, even without in-person interaction [8
]. When an individual outside of the state expressed interest in attending the Cytoscape workshop, the librarians decided a remote training session via webcast might be a valuable instructional format for reaching a broader audience, even though this type of training would lack the in-person component of the class.
The librarians developed a remote session that was first offered in March 2011 (). The advantage of the additional format was to expand the audience, both within the University of Michigan and beyond the physical bounds of the school. Adobe Connect software, which was already licensed centrally by the university, was used to allow attendees to remotely stream the session from their own computers. The librarians had free access to a seminar room that had the existing technology hardware infrastructure and personnel support for Adobe Connect.
Attendees were asked to register to attend this remote session to allow the librarians to gather contact information for pre-training and post-training information and follow up. Before the day of the session, a librarian sent registrants a link to a web page containing the link for viewing the live session, along with course handouts. Because hands-on time was difficult to accommodate for a remote session, the session length was curtailed to one hour. A text chat box, staffed by a second librarian, was available for attendees to ask questions. The session was recorded to allow other interested individuals to view it in the future. As a result, the recording has been sent to several people outside of the University of Michigan who have expressed interest in Cytoscape training and has been posted on the Training web page of the National Resource for Network Biology [9
]. The session recording also provided a point-of-need training format for researchers who were unavailable during the scheduled live remote session but could view the recording at a time that was convenient and useful for them.