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Meeting Records: From 29 July
Date: 29th July 2021
Participants: PMR, Ayush, Shweata, Chaitanya, Sagar
Key Points:
- pyami smoke test
- Debugging pyami.py
- Replacing unicode characters in text file
- Ayush: INYAS presentation, Collect previous presentations.
- Chaitanya: Meeting with Ambreen and use her approach, Will manage college and internship.
- Sagar: Detailed recording on wikipage required, Handling one dictionary at a time, Discussion with Gita Maa’m on eoGene and plant secondary metabolite dictionaries.
Date: 2nd August 2021
Participants: PMR, GY, Shweata, Chaitanya, Sagar
Key Points:
- INYAS Presentation.
- Creating dictionary for phrase extraction from TPS papers.
- Logbook reporting for each dictionary.
- Goldstandard for terpene synthase/TPS query
Date: 5th August 2021
Participants: PMR, Shweata, Ayush, Sagar
Meeting record:
- Shweata: Checking data availability for TPS corpus papers.
- Sagar: Improve “TPS Corpus” with supplimentatry, PMC hyperlinks, Checking location of keywords in free txt, fig, table. Setup rules for scooping
- INYAS presentation: Ayush will prepare presentation.
Date: 9th August 2021
Participants: PMR, GY, Shweata, Ayush, Sagar, Chaitanya
Meeting record:
- Sagar: Downloading all supplementary, documenting with readme. file, 2 pictures for INYAS presentation
- Shweata: will prepare presentation
- Chaitanya: Manually label 1000 sentences for oil1000, Picture for INYAS presentation.
- Ayush: will prepare presentation
Date: 12th August 2021
Participants: PMR, GY, Shweata, Ayush, Sagar, Chaitanya
Meeting record:
- Shweata and Ayush will record their own INYAS presentations.
Date: 16th August 2021
Participants: PMR, GY, Shweata, Ayush, Sagar
Meeting record:
- Fitting INYAS interns.
- Need to discuss (Sagar and Shweata) TPS project for 5 interns
- Docanalysis
- Freezing pyami
- Review docanalysis and pyami in next meeting.
Date: 23rd August 2021
Participants: PMR, Shweata, Ayush, Sagar, Chaitanya
Meeting record:
- Discussed the components for demo on Wed. Proof of Concept (demo based on say 5-10 papers - emphasize scalability)
Date: 26th August 2021
Participants: PMR, GY, Shweata, Ayush, Sagar, Chaitanya, Karya Intern and NIPGR Intern
- NIPGR and KARYA Interns: Welcome of KARYA interns,
- Interns need to report What they did, Going to do, what is blocking, Karya intern should learn to install software during 1-2 weeks
- Karya Intern: Welcome of Anam, Prachi, Gargee, Anjali,Rageshwari
- NIPGR Intern: Welcome of Utkarsha, Ankit, Anubh. NIPGR interns can help karya interns
Date: 30th August 2021
Participants: PMR, GY, Shweata, Ayush, Sagar, Chaitanya, Karya Intern (except Anam) and NIPGR Intern (except Utkarsha)
- Installing pygetpapers and pyami
- Dictionaries installation (big files problem because of different versions).
- Assigned miniprojects to KARYA interns.
- Chaitanya officially completed the duration for internship. He will be volunteering.
Date: 2nd September 2021
Participants: PMR, GY, Shweata, Ayush, Sagar, Karya Intern (except Prachi, Anjali) and NIPGR Intern
- Ayush: Paper writing, discussed config file requirement. Explained use of pygetpapers
- Sagar: Update table with software installation, Handle meeting next week.
- NIPGR Interns: Interns are requested to give their innovative inputs into crop5 project. Ankit explained precision and recall (for question on creating a list of stop words)
- Ankit and Anuv will help Rageshwari with pygetpapers installation.
Date: 6th September 2021
Participants: Sagar, Karya Intern (except Anjali) and NIPGR Intern (except Anuv)
- NIPGR and KARYA Interns: Interns are requested to give their innovative inputs into crop5 project.
- Discussion with KARYA interns on miniprojects
- Confirmed software installation and wikipage of each intern.
- Discussion with NIPGR interns on project ideas and documentation.
- Reporting daily stand ups.
Date: 9th September 2021
Participants: Sagar, KARYA Intern (except Anjali) and NIPGR Intern (except Prathmesh)
- Ankit+Utkarsha is working on Tomato metadata analysis
- Prachi created TPS dictionary. All KARYA interns will create and test dictionary.
- Anuv will work on citrus metadata analysis. Pooja didn't joined.
- Shweta introduced metadata analysis script and answered intern’s questions.
- Ayush explained pyami installation and its status.
- We solved some of Ami3 installation difficulties in mac because of upgraded version.
Date: 13th September 2021
Participants: Shweata, Sagar, KARYA Intern (except Rageshwari) and NIPGR Intern (except Utkarsha)
- Welcome of Pooja Yadav and assigned miniproject Citrus with Anuv.
- I sent text classification and machine learning related 4 papers to NIPGR interns.
- Prathmesh documented and discussed project idea https://github.com/petermr/crops/wiki/Progress-Report:-Prathmesh-Sharma .
- Prathmesh presented a paper https://pubs.acs.org/doi/10.1021/acs.jcim.0c00409 . He is trying to analyse Rice TPSs sequence with autoBioSeqpy to find something new.
- Anuv presented a paper on machine learning applications in bioinformatics and discussed project idea.
- Prachi and Anam gave demo of dictionary creation to Anuv, Prathmesh
Date: 16th September 2021
Participants: Shweata, Sagar, Ayush, PMR, KARYA Intern (except Pooja) and NIPGR Intern (except Ankit)
- Plant-compound-tps name - linking nodes, Visualising this information
- PMR introduced the project.
- Everyone introduced themselves.
- Checked the wikipages of all interns (gave Github access to crop repo).
Date: 20th September 2021
Participants: PMR, Sagar, Ayush, KARYA Intern (except Pooja) and NIPGR Intern (except Prathmesh)
- Interns must put Wikipage link in standup if relevant
- Attendance is important.
- Traffic light for software testing : amidict, pygetpapers, docanalysis, pyami, metadata analysis (https://github.com/petermr/CEVOpen/wiki/KARYA-Intern-Projects)
- Sagar will prepare 15 min. presentation on terpene chemistry
- Interns will explore SPARQL query