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. ![]()
Features
Use cases ![]() 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 Effective
teaching aid (web-based learning,
teaching and evaluation tool). Can expand educators repertoires by
enabling distance learners to participate and collaborate in creating concept maps and mind maps.
Effective for teaching of new concepts ( about pathways, disease mechanism or
drug action ). In addition, they can assist educators and trainers in
supervising and evaluating student. Assess students' understanding of the
subject topic. Meaning-making effective linking of new
knowledge to old knowledge (existing manually curated pathways). KcPAVS
allow this process to occur more readily.
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. ![]() Screen shots: Annotation of pathway with shapes, text, charts and images <under construction> Demonstration <under construction> |
KCPAVS features >