Time Log - GeorgeIniatis/Blood_Brain_Barrier_Drug_Prediction GitHub Wiki
Project Details
- Project Name: Predicting drugs that can cross the blood-brain-barrier
- Student Name: George Iniatis
- Student ID: 2329642
- Supervisor: Dr. Jake Lever
Week 2
30 Sep 2021
- 2 hours Reading the project guidance notes
- 2 hours Brain-storming and looking at ML
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
3 Oct 2021
- 2.5 hours Literature review
Week 3
4 Oct 2021
- 2 hours Literature review
7 Oct 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
8 Oct 2021
- 2.5 hours Restructuring of Research Journal
9 Oct 2021
- 3 hours Literature review
10 Oct 2021
- 3.5 hours Literature review
Week 4
11 Oct 2021
- 2 hours Literature review
12 Oct 2021
- 2 hours Literature review
- 1.5 hours Dataset exploration. Noticed some abnormalities when comparing data with PubChem database
14 Oct 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
15 Oct 2021
- 2 hours Setting up PyCharm and fixing errors
- 3.5 hours Writing some code and getting familiar with PubChem API
16 Oct 2021
- 2.5 hours Some debugging and refactoring of the code
- 0.5 hour Manually searching some compounds that couldn't be searched by the code. Led to me figuring out the special characters problem
17 Oct 2021
- 0.5 hour Writing some code to use POST requests for SMILES with special characters
- 0.5 hour Code refactoring
- 1 hour Getting familiar with RDKit and setting up Anaconda Environment
- 0.5 hour Looking at SIDER database
Week 5
18 Oct 2021
- 0.5 hour Writing some code to use GET requests to populate chemical descriptors
- 1 hour Code refactoring and some brainstorming on how to use SIDER database
19 Oct 2021
- 2 hours Writing some code to integrate SIDER datasets and get side effects
- 0.5 hour Had a look at Google Searches
- 2 hours Dataset work
- 0.5 hour Updating wiki
- 2 hours Debugging a json related bug
20 Oct 2021
- 2.5 hours Dataset work
- 0.5 hour Updating wiki
21 Oct 2021
- 0.5 hour Making Side_Effects json compatible
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
- 0.5 hour Updating wiki
- 2 hours One hot encoding for side effects
- 1 hour Integrating Indications dataset and creating a one hot encoding
22 Oct 2021
- 2.5 hours Automated Google Searches. Led me to discovering a really important bug
- 2.5 hours Debugging and repopulating dataset
23 Oct 2021
- 2 hours Trying to get some results from Google Searches. Google seems to only allow a certain number of results to be retrieved
24 Oct 2021
- 1 hour Automated google searches coding
Week 6
26 Oct 2021
- 5 hours Automated google searches coding
- 0.5 hour Updating wiki
27 Oct 2021
- 3 hours Automated google searches coding
- 1.5 hours Manual verification of results
28 Oct 2021
- 0.5 hour Updating wiki
- 2 hours Site targeted google searches
- 1 hour Manual verification of results
29 Oct 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
- 0.5 hour Working on presentation
- 1.5 hours Manually verifying google searches
- 1.5 hours PubMed API
30 Oct 2021
- 3 hours PubMed API
31 Oct 2021
- 0.5 hour Working on presentation
- 0.5 hour Regular expression calibration
- 0.5 hour Manually verifying results from PubMed searches
Week 7
1 Nov 2021
- 0.5 hour PubMed API calls coding
- 1 hour Manually verifying results from PubMed Central searches
- 0.5 hour Updating the Wiki
2 Nov 2021
- 0.5 hour Group meeting with supervisor and other students
- 2.5 hours Trying to use Elsevier API. Unable to do so
3 Nov 2021
- 1.5 hours Looking at Springer APIs
4 Nov 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Fixing Multiple SMILES issue
- 6 hours Springer API work and PubMed API refactoring
5 Nov 2021
- 0.5 hour Writing meeting minutes and plan of action
- 0.5 hour Fixing bug in PubMed API calls. Need to rerun PMC searches
- 1 hour Springer API work
- 2 hours Manually verifying searches
6 Nov 2021
- 1 hour Manually verifying searches
Week 8
11 Nov 2021
- 0.5 hour Meeting with supervisor
- 1 hour SK-Learn tutorial video. Wasn't really helpful
- 3 hours Datalore exploration
12 Nov 2021
- 0.5 hour Writing meeting minutes and plan of action
- 2 hours SK-Learn tutorial video. Extremely helpful
Week 9
18 Nov 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
- 2 hours Working on visualisations
19 Nov 2021
- 3 hours Datalore work
Week 10
23 Nov 2021
- 1.5 hours Datalore work and UMAP implementation
- 1 hour Model work
- 1 hour Looking at metrics
24 Nov 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
25 Nov 2021
- 2 hours Brainstorming about the model categories and splitting data into test sets
- 2 hours Brainstorming and writing the Machine Learning Journal
Week 11
2 Dec 2021
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
Week 12
7 Dec 2021
- 2 hours Project information session
Week 13
15 Dec 2021
- 2 hours End of Semester 1 Status Report
19 Dec 2021
- 1 hour Datalore work
Week 14
20 Dec 2021
- 1 hour Brainstorming about models
21 Dec 2021
- 2 hours Model work
22 Dec 2021
- 1.5 hours Model work and RFECV
23 Dec 2021
- 1.5 hours Model work
Week 15
27 Dec 2021
- 2 hours Model work
28 Dec 2021
- 0.5 hour Read ML columns
29 Dec 2021
- 0.5 hour Went through the research journal
30 Dec 2021
- 2 hours Model work
31 Dec 2021
- 2 hours Model work
02 Jan 2022
- 0.5 hour Plotly
Week 16
06 Jan 2022
- 2 hours Model work and reading articles
07 Jan 2022
- 1.5 hours Y-Scrambling
08 Jan 2022
- 4 hours Y-Scrambling and Code Refactoring
- 1 hour Creating tables
09 Jan 2022
- 2.5 hours Permutation Testing and Code Refactoring
Week 17
10 Jan 2022
- 2 hours Permutation Testing and Creating Tables
11 Jan 2022
- 1 hour Updating ML journal
12 Jan 2022
- 0.5 hour Meeting with supervisor
- 0.5 hour Writing meeting minutes and plan of action
14 Jan 2022
- 1 hour Streamlit application basics setup
15 Jan 2022
- 2 hours Streamlit app progress
16 Jan 2022
- 4 hours Streamlit app work
Week 18
17 Jan 2022
- 4.5 hours Streamlit app work
18 Jan 2022
- 4.5 hours Streamlit app work
19 Jan 2022
- 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action
Week 19
24 Jan 2022
- 2 hours Streamlit app work
25 Jan 2022
- 3 hours Looking at error analysis
26 Jan 2022
- 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action
Week 20
31 Jan 2022
- 3 hours Error analysis work
01 Feb 2022
- 5 hours Error analysis work
02 Feb 2022
- 1 hour Meeting with supervisor & Writing meeting minutes and plan of action
05 Feb 2022
- 3 hours LIME
- 2.5 hours Updating Streamlit App
06 Feb 2022
- 3.5 hours Updating Streamlit App
- 1 hour Making python files csv friendly
Week 21
08 Feb 2022
- 3 hours Dissertation work - Introduction
09 Feb 2022
- 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action
- 2.5 hours Dissertation work - Background
13 Feb 2022
- 3 hours Dissertation work - Background
Week 22
14 Feb 2022
- 3.5 hours Dissertation work - Background
15 Feb 2022
- 4 hours Dissertation work - Background
16 Feb 2022
- 3 hours Dissertation work - Requirements Analysis
19 Feb 2022
- 4.5 hours Dissertation work - Requirements Analysis
20 Feb 2022
- 4 hours Dissertation work - Requirements Analysis
Week 23
21 Feb 2022
- 3 hours Dissertation work - Requirements Analysis
23 Feb 2022
- 3 hours Dissertation work - Design & Implementation
25 Feb 2022
- 2.5 hours Dissertation work - Design & Implementation
26 Feb 2022
- 3 hours Dissertation work - Design & Implementation
27 Feb 2022
- 3 hours Dissertation work - Design & Implementation
Week 24
28 Feb 2022
- 2.5 hours Dissertation work - Results & Evaluation
01 Mar 2022
- 3 hours Dissertation work - Results & Evaluation
02 Mar 2022
- 1.5 hours Organising repo
03 Mar 2022
- 2 hours Organising repo
05 Mar 2022
- 3 hours Dissertation work - Results & Evaluation
06 Mar 2022
- 3 hours Dissertation work - Results & Evaluation
Week 25
07 Mar 2022
- 3 hours Dissertation work - Conclusion
08 Mar 2022
- 4 hours Dissertation work - Checking
10 Mar 2022
- 1 hour Dissertation work - Checking
11 Mar 2022
- 1 hour Dissertation work - Checking
Week 26
16 Mar 2022
- 0.5 hour Meeting with supervisor & Writing meeting minutes and plan of action
Week 27
27 Mar 2022
- 2 hours Dissertation work - Abstract & Final adjustments
28 Mar 2022
- 2 hours Dissertation work - Final adjustments
29 Mar 2022
- 5 hours Dissertation & Presentation Work
30 Mar 2022
- 4.5 hours Presentation Work & Submission