Collaboration tools in KcPAVS provides a flexible visual environment for structuring (brainstorm, collect, organize), presenting, and sharing digital information in context of biological processes and pathways.

1. Search for pathway(s) of interest
2. Annotate a pathway
   
• suggest an idea 
  
• ask questions
  
• mark important facts
  
• overlay analysis results
3. Use hierarchical commenting system to include detailed notes with references
   
4. Collaborate and Communicate
   
• engage in discussion with peers
• exchange annotations notes
  
• review, edit / correct annotations and send it back to peers
• comment ( supports hierarchical comments)  on the annotations
  
• quiz students
• teach and discuss
• Export the context, create links to annotation-file.
• email links to annotation-file or download and email the annotation file
  
• import and/or merge annotation files; recreate / get back the context and annotations
  
5. Publish
• make the annotation-files available to others on a digital repository (e.g. Google docs file repository, Fedora, Sakai,)
  

Features

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• Zooming and Panning 
• Drawing and Editing – create and delete annotations (Annotate using symbols from large biological concept library, text, shapes, lines and charts); change color and text size;  editing text, moving, auto-saving annotation
• Plan large scale, reuse the existing knowledge, connect past knowledge to present idea or concepts
• Assigning annotations to a pathway or specifically to component itself
• Include detailed notes, references, hyperlinks for every annotation added. Add pictures, add links to audio and video
• Add references, import reference details from PubMed via web-services, references are listed against comments separate tab for easy access.
• Can also include overlays laid to visualize the pathway analysis results.
• Export and download the annotations as BioPAX file.
• Save annotation on our server and generate link to the file.
•  The annotated file can be either downloaded, emailed as attachment or a link can be sent to other party.
• Collaborating online is simple and fast.
• Comment on a topic, organizes comments hierarchically, every comment has numbering ( multilevel numbering). Organize your coment by creating a Child Node beneath the Primary Node. Then create a Child Node beneath that one, and so on. In this way, your ideas will remain categorized in nestled trees that are visually clear from other ideas, documents and files.
  
• Get feedback and opinion from multiple collaborators. Each collaborators can edit their own maps and then it can be sent to a single co-ordinator who could consolidate all the data into one map.
  
• Import single annotation file or multiple annotation file, auto-merge comments and annotations file while importing. Import will recreate each of the annotations as was provided by the original author.
  
• Extract sub network associated with annotated pathway components and visualize in Cytoscape

Use cases

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Researchers can discuss, learn and exchange ideas

Brainstorming and collaboration is simple and easier. Draw/illustrate your ideas using text, symbols, charts and shapes. Not only can you visualize your thoughts, but you can also collaborate with peers on a task online. Record ideas, organize your thoughts, save ideas and share them with peers. The shared maps can also include overlays laid to visualize the pathway analysis results. Collaborators can edit their own annotation-maps, comment on an topic and then sent to the co-ordinator who could consolidate multiple annotation-maps into one map. Group can debate over a topic relating to a pathway and record the conversations as hierarchical comments.

A novice researcher can post questions/propose an hypothesis using a pathway(s) and send it to researcher B (expert /  colleague / adviser ) who could add comments. All the comments and input Information is stored as hierarchical tree. Comments can be added under any particular previous comment or as new comment. The comments/Information that could be included inside notes can be formatted text, hyperlinks (webpage, file on the web), PMIDs or complete citations. Such updated annotated document can be sent back to researcher A. To and fro exchange of document can go on till the intended purpose is met.

See Video and screen shots: Planning experiments about calcium signaling pathway in mouse cardiomyocytes


<coming soon: software demo here>


In the demo a expert uses KcPAVS to design experiments in relation to calcium signaling pathway and also includes references to protocol and links to company site from where the materials needed for experiments could be procured.. After planning and annotation is complete he downloads annotation-file (BioPAX format) and sends to his colleague via email. Upon receiving the file the colleague will import the sent file into KcPAVS, which will recreate all the annotations notes exactly as it was put by the expert.

Figure 2: Communicating simple molecular mechanism. Sequence of the inhibitor peptide  and other details like citation of the publication from which sequence was obtained is mentioned. this annotations can be exported and sent to collaborator. Collaborator can import the annotation file and see all the details as is in the figure.



Teaching and quizzing students


Teachers can use this tool as teaching aid or for quizzing. Questions can be prepared and the document can be sent to student. Students can answer and return it back to teacher who can then evaluate and grade students response. Teacher can also merge the student answer-file with the correct-answers and return them. Which will help students to learn retrospectively.

Figure 3: Screen shot of quiz session. The questions posed by teacher in a quiz were answered by student and subsequently comments were added by teacher for wrong answers.




Making small sized personal/group knowledge bases / notes

Structure of pathway provides a framework for systematic brainstorming ideas, gathering, organizing and maintaining information about proteins, interactions and pathways along with references, links to web pages and files on the web.
This feature allows researchers to organize their ideas and data in a non-linear format guided by pathways as framework that facilitate creative problem solving. Scientists, students and physicians can quickly transform a jumble of ideas , links to collected documents, files, video, audio and any other information into one seamless mind map (save it all in one file) -- giving them access to their most valuable data related to pathways from one place. Researches in a group can make their annotation-files available to others by uploading them to digital repositories / libraries or LMS systems on which you have an account and /or publishing privileges. Since the annotation files include a detailed context around each added annotation, the search tools on a computer or hosted servers can query pathway components and its associated notes and links. For example searching for a protein name/pathway name/interaction name will return all the annotation-files which contains that keyword.

Reporting error and suggesting corrections to a pathway

If you found an error or want to inform an update about a pathway. Use this tool to generate a visual report with all relevant details ( e.g. notes and citations), export the annotation-file and send us (support@cidms.org) we will compile them together and report it to KEGG periodically.Work flow of community collaboration by annotating pathways ( visual and text objects) and exchange ideas

Annotation of pathway with shapes, text, charts and images

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