Client: Wilson Leung: wleung(at)wustl.edu
Project: Distributed Blast for Classroom Teaching
Core technology: https://sequenceserver.com/
- Has the GUI and BLAST framework required for teaching.
- Source: https://github.com/wurmlab/sequenceserver
- Reference material: Blast in the cloud: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast (note – this may not be needed)
- Can help understand the resource requirements for blast
- Using pubic Blast searches can get overloaded/throttled when used in a classroom by many students
- Results can change due to updates to the underlying databases of sequences being searched.
- While SequenceServer is a useful framework for teaching blast, deploying it at scale for a classroom is beyond what most instructors (e.g., high school, PUI) can do
- -->Easily deployable version of Sequence Server for scaling<--
- The client requires a web client which can be used by educators and students to run the NCBI BLAST Basic Local Alignment Search Tool algorithm.
- The client would specifically like for us to provide the wurmlab/sequenceserver local web front-end version of the BLAST tool, which delivers the user interface and analysis capabilities they require.
- Finally the client needs the hosted blast implementation to support multiple classes of at least 100 students all using the BLAST curriculum concurrently (courtesy of Wilson's slides), with an average run time of 2-3 minutes per job. As well as some assurance that the ~100 jobs will finish at approximately the same time.
- Instructors add/build their datasets to Sequence Server
- Image/deployment can scale as required by the number of students in the class
- Bonus: Caching results for the same query
- Bonus: Updates to UI (need more specification from client)
Questions for client: https://hackmd.io/qG-zXUK-Q0SY7f2YI3xXcw?both
User Stories: What are the type of people who will use this project
- High school students (using the system)?
- Undergraduate students (using the system)?
- Graduate students?
- Researchers (bigger datasets and analysis)?
- Teachers (setting up the system for classes)?