Module 1 and 2:
1. Overview of things learned:
- Technical Area:
- Deeper understanding on bioinformatic and the process of research paper for later replication.
- Getting use to the concept of dependency parsing and dependency matrix
- Learning to retrieve data for replication
- Tools:
- Git for team coding collaboration
- vscode as ILE
- pubmed parser for reading .xml file from Pubmed
- spacy for tokenization drug-gene name and relationships
- Stanford parser for dependency parsing
- Soft Skills:
- Team work and communication
- Task management and assignment
- Sprint work scheme
- Journal club
2. Three achievement highlight
- Implementing pubmed parser, spacy and Stanford parser correctly
- Getting familiar with new environment vscode and Github
- Planning and assigning tasks effectively among team to achieve desired results
3. Goals for upcoming week
- Understanding and applying EBC algorithm
- Learning Docker and AWS
4. Detailed statement of tasks done
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Understanding and retrieving required databases for replication (except Drugbank due to account verification)
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Setting up the working pipeline for the team to keep in track and in the same page
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Hurdles:
Different timezone: difficult for the whole team to set up group meeting => recording meeting and documenting for later review; dividing sub-team with closely timezone
Understanding new concepts in bioinformatic and NLP: all members have no prior knowledge on bioinformatic, also each member have own level in technical area, so that sometimes we’re not in the same page => learning new knowledge in Journal club style is more efficient and consuming; dividing tasks based on required skills so each member can choose what he/she want to take responsible for; reaching out for the mentors when unsure or need help
