# Bioinformatics Team Meetings

[Previous Check ins - March 2021](https://hackmd.io/-DXVadqmQuuh7F3g_M_6JQ) and [Previous Check ins - November 2021](https://hackmd.io/1Jh94XV-SKOWRKzJex5Qxg)

[Teams Meeting Link](https://teams.microsoft.com/l/meetup-join/19%3a6887c23962c248a89124009c0cef2fe9%40thread.tacv2/1634224213244?context=%7b%22Tid%22%3a%22a4e98fb5-57d9-4b97-b7b2-60ab87e9a234%22%2c%22Oid%22%3a%226c8af0b1-c61b-49ce-9ee9-2dbbcb9d6bed%22%7d)

### About the format:
- You have three minutes at most.

## Copy the content below and provide an update

#### Who did you help this week?

#### Who helped you this week?

#### What did you achieve last week?

#### What did you struggle with?

#### What would you like to work on this week?

#### Where do you need help?

# March 21st 2022
## Hello & Check-in
1. Ruth Nanjala
2. Ken Mugambi
3. Gladys Rotich
4. Nyasita Ondari
5. Alex Gashanja
6. Karega Pauline
7. Caleb Kibet
8. Maxwell Booker
9. Audrey Oronda

**Ruth Nanjala**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- Laura, Ken, Pauline
_What did you achieve last week?_
- Assisting the interns with code debugging
- Instructing the UCT Carpentries workshop
- NGS staff training
- NIT Carpentries Instructors meetup
- Internship Manuscript
- BOSS conference planning
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Coordinating the internship activities
- Assisting with design of the Interns miniprojects
- Internship manuscript
- Imputation manuscript
- BOSS conference planning
- H3ABioNet & Wellcome Connecting Science NGS training
- Carpentries community call
_Where do you need help?_
- None
**Ken Mugambi**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- Caleb
_What did you achieve last week?_
- Assisting the interns with code debugging
- Project objective 2
- H3bionet meeting
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Project - objective 2

**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Pauline
_What did you achieve last week?_
- Data analysis, BWCB networking
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis
- Instructor carpentries training
_Where do you need help?_
- None

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- Oscar
_What did you achieve last week?_
- Data analysis
- plot vector model
_What did you struggle with?_
- None
_What would you like to work on this week?_
- plot host model
- model analysis
_Where do you need help?_
- None

**Alex Gashanja**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- Data organization
_What did you struggle with?_
- None
_What would you like to work on this week?_
- finish Data organization
- meet supervisor
_Where do you need help?_
- none

**Caleb Kibet**
#### Who did you help this week?
- My students, Pauline, and Ruth
-
#### Who helped you this week?
- Pauline, Ruth

#### What did you achieve last week?
- Planning for the BOSS Conference
- Writing: manuscript, proposal
- OLS and OBF meetings

#### What did you struggle with?
- NA

#### What would you like to work on this week?
- Presentations for H3ABioNet an diveRSE
- Revise the ICT Taskforce report
- Interns projects
-
#### Where do you need help?

**Denis Kinyugo**
#### Who did you help this week?
- NA

#### Who helped you this week?
- Pauline, Ruth, Ken

#### What did you achieve last week?
- Working on the mini project

#### What did you struggle with?
- Obtaining tools
- Obtaining data

#### What would you like to work on this week?
- Mendley workshop
- Presentation
#### Where do you need help?
- NA

**Maxwell Booker**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Laura and Ruth
_What did you achieve last week?_
- Worked on the paper I am to reproduce
_What did you struggle with?_
- Getting relevant versions of softwares
_What would you like to work on this week?_
- Information Literacy training
- Working on the Miniproject
_Where do you need help?_
- None

**Audrey Oronda**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Kinyugo, Pauline, Ruth, Ken
_What did you achieve last week?_
- Worked on the mini project
- Presented on Journal Club
_What did you struggle with?
- Getting the data
- Tools for constructing a pseudogenome
_What would you like to work on this week?_
- Information Literacy training
- Finalizing on the Miniproject
_Where do you need help?_
- None

# March 14th 2022
## Hello & Check-in
1. Gladys Rotich
2. Alex Gashanja
3. Maxwell Booker
4. Audrey Oronda

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- Caren
_What did you achieve last week?_
- Linear regression to achieve objective 2
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Acquire data
- Plot models
_Where do you need help?_
- None

**Alex Gashanja**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- learnt how to use bedtools
- Phylogenetics
_What would you like to work on this week?
- Extract genes from genomes
- learn phylogenetics
_Where do you need help?_
- Phylogenetics

**Maxwell Booker**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Laura
_What did you achieve last week?_
- Worked on the paper I am to reproduce
_What did you struggle with?_
- Getting relevant versions of softwares
_What would you like to work on this week?_
- Working on the paper I am to reproduce
_Where do you need help?_
- None

**Audrey Oronda**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Ken, Pauline, Kinyugo
_What did you achieve last week?_
- Understand the paper I am to reproduce
- Working on the paper I am to reproduce with my partner Kinyugo
_What did you struggle with?_
- Understanding some phylogenetic analysis steps
_What would you like to work on this week?_
- Reproducing the paper
- Journal club presentation
_Where do you need help?_
- N/A

# March 7th 2022
## Hello & Check-in
1. Ken Mugambi
2. Maxwell Booker
3. Gladys Rotich
4. Nyasita Ondari
5. Audrey Oronda

**Ken Mugambi**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- Objective 2 on my project
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Meet my supervisors
- Work on Objective 2
_Where do you need help?_
- None

**Maxwell Booker**
_Who did you help this week?_
- Sharon , Audrey
_Who helped you this week?_
- Dr.caleb, Ruth, Pauline, Denis
_What did you achieve last week?_
- Completed my Assignments
- Introduction to Data Science and Machine Learning
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Work on the paper i am to reproduce
- Work on what I have learnt so far
_Where do you need help?_
- N/A

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- Met my supervisors
- Continue with objective 2
_What would you like to work on this week?_
- Acquire missing data
- plot the models
_Where do you need help?_
- None

**Audrey Oronda**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Dr.caleb, Ruth, Kinyugo, Maxxwell
_What did you achieve last week?_
- Introduction to Data Science and Machine Learning
_What did you struggle with?_
- Coding with python
_What would you like to work on this week?_
- Work on the paper I am to reproduce
_Where do you need help?_
- N/A

**Nyasita Ondari**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- Objective 2 on my project
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Meet my supervisors
- Work on Objective 2
c

# February 28th 2022
## Hello & Check-in
1. Ruth Nanjala
2. Gladys Rotich
3. Ken Murithi
4. Nyasita Ondari
5. Denis Kinyugo
6. Alex Gashanja
7. Rodney Omukuti
8. Maxwell Booker
9. Sharon Watiri
10. Audrey Oronda

**Audrey Oronda**
Who did you help this week?

- Maxwell
Who helped you this week?
- Laura, Ruth and Rodney
What did you achieve last week?
- I was able to learn about Phylogenetics, R and Nextflow and Conflict resolution
What did you struggle with?
- N/A
What would you like to work on this week?
- Python, R ,mini-project
- HPC, Data Science and Machine Learning
Where do you need help?
- N/A

**Sharon Watiri**

_Who did you help this week?_
- Rodney

_Who helped you this week?_
- Laura, Ruth, Dennis
_What did you achieve last week?_
- R, Nextflow, Phylogenetics
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Assignments, Machine learning and data science, how to use the HPC
_Where do you need help?_
- N/A

**Rodney Omukuti**
_Who did you help this week?_
- Audrey, Sharonne
_Who helped you this week?_
- Pauline, Laura, Ruth
_What did you achieve last week?_
- R, Nextflow, Phylogenetics
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Assignments, Machine learning
_Where do you need help?_
- N/A

**Maxwell Booker**
_Who did you help this week?_
- Rodney
_Who helped you this week?_
- laura, Ruth and Audrey
_What did you achieve last week?_
- I was able to learn about Phylogenetics, R and Nextflow
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- All Assignments
- HPC, Data Science and Machine Learning
_Where do you need help?_
- N/A

**Ruth Nanjala**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- Pauline, Laura
_What did you achieve last week?_
- Teaching
- Editing my GitHub repo
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Teaching
- John's project
_Where do you need help?_
- Teaching

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- SI model for the vector
- Prepare for JC presentation
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Meet my supervisors
- JC presentation
- Continue with model building
_Where do you need help?_
- Parameter estimation

**Ken Mugambi**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- Objective 2 on my project
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Meet my supervisors
- Work on Objective 2

_Where do you need help?_
- N/A

**Nyasita Ondari**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Teaching
- Finishing up on my analysis of 1st dataset
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Data analysis
- Meeting with supervisors
_Where do you need help?_
- N/A

**Alex Gashanja**
_Who did you help this week?_
- None
_Who helped you this week?_
- Laurah and Ken
_What did you achieve last week?_
- Further annotation of the genomes
_What did you struggle with?_
- Annotation
_What would you like to work on this week?_
- Annotation
- Have a discussion with my supervisors
_Where do you need help?_
- how to use my space in the hpc and maximise it

**Denis Kinyugo**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Nextflow
- R programming
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- High performance computing
- Data Science
- Machine Learning
_Where do you need help?_
- N/A

# February 21st 2022
## Hello & Check-in
1. Ken Mugambi
2. Nyasita Ondari
3. Gladys Rotich
3. Denis Kinyugo
4. Alex Gashanja
5. Maxwell Booker
6. Rodney Omukuti
7. Ruth Nanjala
8. Audrey Oronda

**Audrey Oronda**
Who did you help this week?

- N/A
Who helped you this week?
- Kinyugo, Ken, Ruth
What did you achieve last week?
- Introduction to python, presentation skills
What did you struggle with?
- N/A
What would you like to work on this week?
- Practice more on Python
- R programming
Where do you need help?
- N/A
**Rodney Omukuti**
_ho did you help this week?_
- N/A
_Who helped you this week?_
- Ken,Dr. Caleb, Dennis, Andrew, Ruth
_What did you achieve last week?_
- Python programming
_What did you struggle with?_
- N/A
What would you like to work on this week?
- R, Python, Conflict resolution
_Where do you need help?_
- N/A

**Ken Mugambi**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- Caleb; project
- Pauline; manual gene curation
- Interns
_What did you achieve last week?_
- Pattern Discovery and Pattern matching
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Pattern matching
- Machine learning in binding sites verification
- Meet my supervisor
_Where do you need help?_
- N/A

**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Grant review course
- Statistical and metabolomics analysis; 2nd dataset
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Teaching R
- Novel compound drug target verification
- Meet my supervisors
_Where do you need help?_
- N/A

**Denis Kinyugo**
_Who did you help this week?_
- Fellow interns
_Who helped you this week?_
- Dr Caleb
- Ken
_What did you achieve last week?_
- Introduction to Python
- Presentation
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Learn R
_Where do you need help?_
- N/A

**Alex Gashanja**
_Who I helped last week?_
- None
_Who helped me_
- None
_What I achieved last week?_
- journal-club presentation
- Genome annotation
_What I would like to achieve this week?_
- hold a meeting with my supervisors
- continue annotation
_Where I need help?_
- will depend on what this week has for me

**Maxwell Booker**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Ken,Denis
_What did you achieve last week?_
- Learnt Python programming
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Practicing and Perfecting on what i have learnt so far
- R languages
_Where do you need help?_
- Python programming

**Ruth Nanjala**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- Pauline, Caleb, Laura, Ken, Alex
_What did you achieve last week?_
- Teaching
- Thesis corrections
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Teaching
_Where do you need help?_
- Teaching

**Gladys Rotich**

_Who did you help this week?_
- None

_Who helped you this week?_
- Dr. Kiti

_What did you achieve last week?_
- Met my supervisor
- Done corrections on my equations

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Meet my supervisors
- Do the SI model for vector

_Where do you need help_
- Will reach out for help when needed
## Hello & Check-in
1. Gladys Rotich
2. Ken Mugambi
3. Caleb Kibet
4. Alex Gashanja
5. Ruth Nanjala
6. Maxwell Booker
7. Rodney Omukuti
8. Sharon Watiri
9. Audrey Oronda
10. Nyasita Ondari

**Audrey Oronda**
Who did you help this week?_
- Kinyugo
_Who helped you this week?_
- Eric, Ruth and Pauline
- Denis, Rodney, Max
_What did you achieve last week?_
- Got a good understanding of sequence technologies
- An introduction of bioinformatics
- Understood bash
- GitHub
_What did you struggle with?_
- Some BASH concepts
_What would you like to work on this week?_
- Practicing and Perfecting on what i have learnt so far like BASH
_Where do you need help?_
- N/A

**Sharon Watiri**
*Who did you help this week?*
N/A
*Who helped you this week?*
Ruth, Pauline, Erick, Maxwel
*What did you achieve last week?*
Learnt:
the sequencing technologies,
Introduction to BASH
Introduction to Bionformatics
Soft skills
*What did you struggle with?*
N/A
*What would you like to work on this week?*
Reread the provided material
Polish up on Bash
Assignments
*Where do you need help?*
N/A

**Rodney Omukuti**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Eric, Ruth and Pauline
_What did you achieve last week?_
- Understood sequencing technologies
- Introduction to bioinformatics
- Linux
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- To learn more modules as I incoporate what I have ganered so far
_Where do you need help?_
- N/A

**Maxwell Booker**
_Who did you help this week?_
- Sharon
_Who helped you this week?_
- Eric, Ruth and Pauline
- Denis, Audrey and Rodney
_What did you achieve last week?_
- Got a good understanding of sequence techniques
- Got a good introduction of bioinformatics
- Understood bash
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Practicing and Perfecting on what i have learnt so far
_Where do you need help?_
- N/A

**Glady Rotich**
Who did you help this week?
- N/A
_Who helped you this week?_
- Pauline King'ori
- Laurah Nyasita
_What did you achieve last week?_
- Derive ODE's
- Basic SIR model
_What did you struggle with?_
- Estimating model parameters
_What would you like to work on this week?_
- Estimate model parameters
- Meet my supervisors
_Where do you need help_
- Estimating model parameters

**Ken Mugambi**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Caleb; project
- Pauline; Manual gene annotation
_What did you achieve last week?_
- Manual gene annotation
- Pattern Discovery and Pattern matching
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Pattern matching
- Machine learning in binding sites verification
- Meet my supervisor
_Where do you need help?_
- N/A

**Alex Gashanja**
Who did you help this week?
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Gene annotation
- learning commandline blasting
_What did you struggle with?_
- creating blastp database
_What would you like to work on this week?_
- Gene annotation
- Blasting
- Meet supervisors
_Where do you need help?_
- N/A

**Caleb Kibet**

##### Who did you help this week?
- Dr. Masiga
- Ken

##### Who helped you this week?
- Andrew
##### What did you achieve last week?
- Completed a report review
- Finalized on the strategy
-
##### What did you struggle with?
-NA
##### What would you like to work on this week?
- Grant and manuscript writing
-

##### Where do you need help
-

**Ruth Nanjala**
_Who did you help this week?_
- Interns
_Who helped you this week?_
- Pauline & Erick
_What did you achieve last week?_
- Teaching
- Thesis corrections
_What did you struggle with?_
- Citations in Mendeley
_What would you like to work on this week?_
- Teaching
- Breast cancer VUC
- Thesis corrections
_Where do you need help?_
- Teaching

**Denis Kinyugo**
_Who helped you this week?_
- My fellow interns
- Trainers
_What did you achieve last week?_
- Introduction to Bioinformatics
- Introduction to Bioinformatics tools and data sources
_What did you struggle with?_
- Biological concepts that form the basis of bioinformatics
_What would you like to work on this week?_
- Learn more about foundational biological concepts
- Interact with bioinformatics tools and data sources
_Where do you need help?_
- Molecular biology concepts

**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Data analysis
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Statistical and metabolomics analysis; 2nd dataset
- Meet my supervisor
_Where do you need help?_
- N/A
-
# February 7th 2022
## Hello & Check-in
1. Ruth Nanjala
2. Eric Kariuki
3. Ken Mugambi
4. Caleb Kibet
5. Nyasita Ondari
6. Audrey Oronda
7. Sharon Watiri
8. Maxwell Booker
9. Rodney Omukuti
10. Alex Gashanja
11. Denis Kinyugo
12. Gladys Rotich

**Rodney Omukuti**
_Who helped you this week?_
- Dr. Kibet, Ruth and Dennis
_What did you achieve last week?_
- Git and Github
- Onboarding
- Introduction to commandline
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Bash
- Programming
_Where do you need help?_
- N/A

**Ruth Nanjala**
_Who helped you this week?_
- Dr. Kibet, Erick
_What did you achieve last week?_
- Interns final presentation
- Interns onboarding & teaching
- Thesis correction
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Plant pangenome project
- Thesis correction
- Interns
_Where do you need help?_
- Functional annotation using topGo

**Audrey Oronda**
_Who did you help this week?_
N/A
_What did you achieve last week?_
- Interns onboarding
- Introduction to Git and GitHub
- Exploring slack
_What did you struggle with?_
- GitHub command line
_What would you like to work on this week?_
- GitHub command line
- Introduction to bash
- Workflow languages
_Where do you need help?_
- galaxy workflow

**Sharon Watiri**
- Who did you help this week? -
- none
_Who helped you this week?_
- Dr. Kibet, Ruth, Kinyugo
_What did you achieve last week?_
-introduction to Git and Github
_What did you struggle with?
- Command line
_What would you like to work on this week?_
- Reproducibility in Research
- Open Science and data management in Bionformatics
- BASH
- Work on the command line
_Where do you need help?_
- N/A

**Maxwell Booker**
_Who did you help this week?_
- None.
_Who helped you this week?_
- Dr. Kibet, Erick, Ruth
_What did you achieve last week?_
- Learnt and Practiced Command lines.
- Learnt to generate a ssh key.
_What did you struggle with?_
- Command Lines.
_What would you like to work on this week?_
- Practicing Command Lines.
- Bioinformatic Tools and Scripting
- Reproducibility
- Open Science
- Data Management Plan
_Where do you need help?_
- N/A

**Ken Mugambi**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Pauline
_What did you achieve last week?_
- Journal club presentation
- Data analysis
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Data analysis
_Where do you need help?_
- N/A

**Eric Kariuki**
_Who did you help this week?_
- Jacqueline & Rehema, symbiovector project
_Who helped you this week?_
- Dr. Cheseto & Dr. Bargul
_What did you achieve last week?_
- Lab experiments on an ongoing project
- Preparation for a meeting scheduled for 8th Feb
- Worked with John and Oscar on some elements to include on 16S analysis
- Interns final presentation
- Interns onboarding
_What did you struggle with?_
- Lab experiments
_What would you like to work on this week?_
- Moderate the meeting on 8th
- Manuscript writing and analysis
- Interns Teaching; Genomics
_Where do you need help?_
- Lab experiments

**Ken Mugambi**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Caleb; project
- Pauline; Manual gene annotation
_What did you achieve last week?_
- Manual gene annotation
- Pattern Discovery and Pattern matching
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Pattern matching
- Machine learning in binding sites verification
_Where do you need help?_
- N/A

**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Docking experiment
- Data analysis
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Data analysis
_Where do you need help?_
- N/A
-
**Alex Gashanja**
_Who helped you this week?_
- None
_What did you achieve last week?_
- Genome assembly
_What did you struggle with?_
- Annotation
_What would you like to work on this week?_
- Analyse annotated genes
_Where do you need help?_
- None
-
**Denis Kinyugo**
_Who helped you this week?_
- Maxwell Booker, Rodney Omukuti
_What did you achieve last week?_
- Introduction to Git and GitHub
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Introduction to Bioinformatics
_Where do you need help?_
- N/A

**Gladys Rotich**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Data analysis
- Missing Data search
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Data analysis
_Where do you need help?_
- N/A

# January 31st 2022
## Hello & Check-in
1. Ruth Nanjala
2. Nelly Wambui
3. Okeyo Allan
4. Caroline Kogei
5. Gladys Rotich
5.

**Ruth Nanjala**
_Who did you help this week?_
- Interns
- John
_Who helped you this week?_
- Dr. Kibet, Caleb, Pauline, Interns
_What did you achieve last week?_
- John's project
- Interns; code review, soft skills, guidance, writing the internship report
- Breast cancer VUC project
- Streamlined the HLA typing pipeline
- Plant pangenome project
- Thesis correction
_What did you struggle with?_
- Plant genomics project - functional annotation using topGo software
_What would you like to work on this week?_
- Plant pangenome project
- Thesis correction
- Interns
_Where do you need help?_
- Functional annotation using topGo

**Nelly Wambui**

_Who did you help this week?_
- None

_Who helped you this week?_
- Yosef

_What did you achieve last week?_
- Report writing
- Running Yosef's pipeline
- Review of application documents

_What did you struggle with?_
- Yosef's pipeline

_What would you like to work on this week?_
- Final presentation

_Where do you need help?_
- N/A

**Okeyo Allan**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Andrew
- Ruth

_What did you achieve last week?_
- Finished up on building docker image
- Wrote the final report
- Designing PowerPoint
- Running the mbbu pipeline from Github

_What did you struggle with?_
- Running the pipeline using singularity

_What would you like to work on this week?_
- Conduct final project presentation
- Iron out the report and documentations

_Where do you need help?_
- Riview of the presentations

**Eric Kariuki**
_Who did you help this week?_
- Reviewed an application for a former colleague
- Worked with Ruth and Pauline on the Internship report
_Who helped you this week?_
_What did you achieve last week?_
- Performed my lab experiments successfully
- Prepared a presentation ahead of a guest visit at icipe
- Prepared for the thesis defense
- Allocated tasks ahead of data analysis for manuscript writing
_What did you struggle with?_
- Failure of some lab equipment
_What would you like to work on this week?_
- Finalize presentation preparations
- Finalize on proposal defense slides
- Analysis for manuscript writing
_Where do you need help?_
**

**Caroline Kogei**
#### Who did you help this week?

* N/A

#### Who helped you this week?

* Collins and Dr Kennedy helped with model development

#### What did you achieve last week?

* Worked on producing final reports for both the project and my internship journey
* Preparing slides for project presentation
* Writing skills session

#### What did you struggle with?

* Model deployment on the local web
* Identifying tick image data for the model

#### What would you like to work on this week?

* Finalising reports and model optimization
* Model deployment
#### Where do you need help

* N/A

**Gladys Rotich**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Faith
- Dr.Caleb

_What did you achieve last week?_
- Data analysis
- Data acquisition

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Data analysis
- Acquire missing data

_Where do you need help?_
- N/A

# January 24th 2022
## Hello & Check-in
1. Gladys Rotich
2. Caroline Kogei
3. Nelly Wambui
4. Joyce Wangari
5. Nyasita Ondari
6. Okeyo Allan
7. Ken Mugambi
8. Alex Gashanja
9. Ruth Nanjala
9. Collins Kigen
9.

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- Stella
_What did you achieve last week?_
- Met my supervisor
- Data analysis
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Continue with data analysis
- Work on generating a sample model
_Where do you need help?_
- N/A

**Caroline Kogei**
#### Who did you help this week?

* N/A

#### Who helped you this week?

* Nehemiah and Dr Kennedy helped us with our deep learning model
* My fellow interns helped me with editing my powerpoint presentation for the journal club meeting

#### What did you achieve last week?

* Implemented VGG16 and MobileNet keras architectures for our model
* Journal club presentation

#### What did you struggle with?

* Implementing the Inception keras architecture

#### What would you like to work on this week?

* Running the model on tick image data
* Deploying the deep learning model
* Documentation

#### Where do you need help

* N/A

**Nelly Wambui**
_Who did you help this week?_
- None

_Who helped you this week?_
- Yosef

_What did you achieve last week?_
- Writing part of the final report
- Running Yosef's pipeline

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Code Review
- Finish up writing the final report
- Review applications
- Finish up running Yosef's pipeline

_Where do you need help?_
- N/A

**Nyasita Ondari**
_Who did you help this week?_
- None
_Who helped you this week?_
- Alex
_What did you achieve last week?_
- Data analysis; docking
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Continue with data analysis
- Finish docking
- Plant genome miniproject
- Meet supervisors
_Where do you need help?_
- N/A

**Okeyo Allan**
_Who did you help this week?_
- Ken Mugambi
_Who helped you this week?_
- Pauline
- Ken Mugambi

_What did you achieve last week?_
- Automating the pipeline
- Created a test dataset and tested it with the pipeline
- Built our docker image
- Document the work for last week

_What did you struggle with?_
- Running the docker image
- Running the pipeline from github repository
- Automating the pipeline
- Testing the pipeline

_What would you like to work on this week?_
- Figure out how to read file from github repositories
- Figure out why the docker image could not run
- Finish up with the final report
- Have our code review session

_Where do you need help?_
- Figuring out the errors we encountered during last week's work

**Joyce Wangari**
_Who did you help this week?_
- No one
_Who helped you this week?_
- Pauline
_What did you achieve last week?_
- Automating the pipeline
- Started writing our final report
-
_What did you struggle with?_
- running the pipeline with the docker image
_What would you like to work on this week?_
- Fully automating the pipeline
- Finish up with the final report
- Code review session
-
_Where do you need help?_
- Running the pipeline with the docker image

**Ken Mugambi**
_Who did you help this week?_
- None
_Who helped you this week?_
- Allan
_What did you achieve last week?_
- Met my supervisor
- Data analysis
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis
_Where do you need help?_
- N/A
-
-

**Alex Gashanja**
_Who did you help this week?_
- Laurah
_Who helped you this week?_
- None
_What did you achieve last week?_
- Acquired my dataset
- Quality checked my data and trimmed adapters
_What did you struggle with?_
- Trimming overrepresented sequences
_What would you like to work on this week?_
- Continue Data cleaning
- Meet my supervisors
_Where do you need help?_
- N/A

**Eric Kariuki**
_Who helped you this week?_
_What did you achieve last week?_
- Shortlisting and interviewing the next cohort of interns
- Met with my supervisors to discuss the next phase of the project
- Made some progress on the lab experiments
_What did you struggle with?_
- Lab work but got a way around it
_What would you like to work on this week?_
- Prepare for a few upcoming events
- Work on analysis for the manuscript
- Continue with analysis write-ups
_Where do you need help?_

**Ruth Nanjala**
_Who did you help this week?_
- None
_Who helped you this week?_
- Erick, Laura, Ken, Alex
_What did you achieve last week?_
- Met with supervisors
- Thesis defense
- Shortlisting and interviewing the next cohort interns
- Met up with the HLA typing team.
_What did you struggle with?_
- HLA-VBSEQ typing script
_What would you like to work on this week?_
- Interns
- HLA typing project
- Breast cancer project
- Plant genomics project
- John's project
_Where do you need help?_
- N/A

**Collins Kigen**
_Who did you help this week?_
- None

_Who helped you this week?_
- Yosef Hamba

_What did you achieve last week?_
- Writing part of the final report
- Running Yosef's pipeline

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Code Review
- Finish up writing the final report
- Review applications for competitive scholarships
- Finish up running Yosef's pipeline

_Where do you need help?_
- N/A

# January 17th 2021
## Hello & Check-in
1. Ruth Nanjala
2. Ken Mugambi
3. Nyasita Ondari
4. Okeyo Allan
5. Collins Kigen
6. Nelly Wambui
7. Caleb Kibet
8. Joyce Wangari
9. Eric Kariuki
10. Gladys Rotich
11. Caroline Kogei

**Ruth Nanjala**
_Who did you help this week?_
- Interns

_Who helped you this week?_
- N/A

_What did you achieve last week?_
- Code review with the interns
- HLA typing project
- Breast cancer project
- Plant genomics project

_What did you struggle with?_
- N/A

_What would you like to work on this week?_

- Meet up with supervisors
- Thesis defense
- Breast cancer
- HLA typing project

_Where do you need help?_
- N/A

**Nyasita Ondari**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Alex Kimani

_What did you achieve last week?_
- 1st docking experiment
- Boss plant genomics mini-project

_What did you struggle with?_
- N/A

_What would you like to work on this week?_

- Meet up with supervisors
- Repeat docking experiment & MSA

_Where do you need help?_
- N/A

**Okeyo Allan**

_Who did you help this week?_
- Ken Mugambi

_Who helped you this week?_
- Hebrew Simeon
- Ken Mugambi

_What did you achieve last week?_
- Code review
- Automating building snpeff database
- Creating a test config file for testing the pipeline functionality
- Document additional modifications to the mbbu/AAT pipeline

_What did you struggle with?_
- Building the docker image
- Building the speff database

_What would you like to work on this week?_
- Test the pipeline with the test dataset
- Finish up the docker image
- Do a final report on the project

_Where do you need help?_
- Building the docker image

**Collins Kigen**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Ruth Nanjala
- Yosef Hamba

_What did you achieve last week?_
- Succesfully running the MBBU 16S-Accreditation Dada2 pipeline using 3 datasets
- Modified MBBU 16S-Accreditation Qiime2 by introducing flags to a nextflow running command
- Testing the nf-core/ampliseq pipeline using different datasets
- Python practice

_What did you struggle with?_
- N/A

_What would you like to work on this week?_

- Running the pipeline Yosef used
- Having a nextflow script for the MBBU 16S-Accreditation Dada2 pipeline
- Writing of the final report
- Review competitive motivation letter for scholarship

_Where do you need help?_
- Running the pipeline Yosef used

**Nelly Wambui**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Ruth Nanjala
- Yosef Hamba

_What did you achieve last week?_
- Completely running the MBBU 16S-Accreditation Dada2 pipeline using 3 datasets
- Learning how to introduce flags to a nextflow running command
- Testing the nf-core/ampliseq pipeline using different datasets
- Python practice

_What did you struggle with?_
- N/A

_What would you like to work on this week?_

- Running the pipeline Yosef used
- Having a nextflow script for the MBBU 16S-Accreditation Dada2 pipeline
- Writing of the final report

_Where do you need help?_
- Running the pipeline Yosef used

**Joyce Wangari**
_Who did you help_
- N/A
_Who helped you this week?_
- Hebrew Simon
-
_What did you achieve last week?_
- Ran the MBBU pipeline successfully
- python practice
- code review for the mini-project

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Edit the MBBU pipeline
- Start on writing the Final Report
_Where do you need help?_
- building a docker image

**Gladys Rotich**
_Who did you help last week?_
- None
_Who helped you last week?_
- Dr. Daniel Masiga
- Ebhodaghe Faith
_What did you achieve last week?_
- Data access
- Manuscript ammendment for omicscodeathon
- Data analysis
_Where do you need help?_
- N/A
_What did you struggle with?_
- Data access
_What would you like to work on this week?_
- Data analysis
- Meeting supervisors

**Eric Kariuki**
_Who did you help last week?_
- Dr. Yosef on some R tick microbiota analyses
_Who helped you last week?_

_What did you do achieve last week?_
- I submitted my dissertation to the university for examination
- Performed some laboratory work on a previous project
- Met with some of my supervisors
- Interns code review
_What would you like to work on this week?_
- Finish my laboratory experiments
- Find alternatives for missing reagents
- Standardize my analysis scripts
- Meet my supervisors on manuscript writing
_What did you struggle with?_
- Could not get calcium hydroxide required for my lab experiments

**Caleb Kibet**
#### Who did you help this week?

* MSc students at Pwani, and my mentees
*

#### Who helped you this week?

* Received help from Ruth in Keeping the Code Review and interns training on track

#### What did you achieve last week?

* Completed teaching the Pwani University training
* Cleared serveral admin tasks

#### What did you struggle with?

* Balancing betwen the several responsibilities

#### What would you like to work on this week?

* Review interns

#### Where do you need help

* Replace this text with a bullet point list of what you need help.
* It's ok if your list is only one bullet point long!

**Caroline Kogei**
#### Who did you help this week?

* N/A

#### Who helped you this week?

* Nehemiah

#### What did you achieve last week?

* Built a Resnet_50 architecture for our deep learning model.
* Optimising the model's parameters using tensor-board

#### What did you struggle with?

* Implementing the Resnet_50 architecture

#### What would you like to work on this week?

* Optimising the model
* Implementing VGG16 and the InceptionNet architectures
* Identifying a tick Dataset for our model

#### Where do you need help

* N/A

# January 10th 2021

## Hello & Check-in
1. Ruth Nanjala
2. Ken Mugambi
3. Nyasita Ondari
4. Gladys Rotich
5. Okeyo Allan
6. Joyce Wangari
7. Alex Gashanja
8. Caroline Kogei
9. Collins Kigen
10. Joyce Wangari

**Ruth Nanjala**

_Who did you help this week?_
- Interns
- John

_Who helped you this week?_
- N/A

_What did you achieve last week?_
- Code review with the interns
- Helped out with John's project
- HLA typing project

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Breast cancer project
- Meet up with the HLA typing meeting
- Working with the interns

_Where do you need help?_
- N/A

**Ken Mugambi**

_Who did you help this week?_
- Interns

_Who helped you this week?_
- Allan

_What did you achieve last week?_
- Data analysis
- Teaching Python

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Project data analysis
- Working with the interns - python

_Where do you need help?_
- N/A

**Nyasita Ondari**

_Who did you help this week?_
- N/A

_Who helped you this week?_
- N/A

_What did you achieve last week?_
- Proposal submission
- Predicted the structure of TcoHT1 using alphafold
- Started the docking process using Pymol

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Continue with molecular docking using Autodock
- Review results from my isometamidium dataset
- Data analysis (2nd dataset)

**Joyce Wangari**

_Who did you help this week?_
- N/A

_Who helped you this week?_
- Nelly
- Andrew
_What did you achieve last week?_
- Journal club presentation
- continued with the mini-project
- code review for the mini-project

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- mini project
- Msc. application
_Where do you need help?_
- building a docker image

**Nelly Wambui**
_Who did you help this week?_
- Joyce

_Who helped you this week?_
- Dr. Caleb

_What did you achieve last week?_
- Made progress in the Dada2 pipelines
- Tried out more datasets on the nf-core pipeline

_What did you struggle with?_
- Obtaining data containing metadata
- Testing the various pipelines

_What would you like to work on this week?_
- Finish up on testing the pipelines
- Compare the results from Yosef's pipeline and the nf-core pipeline
- Start on the report

_Where do you need help?_
- N/A

**Okeyo Allan**
_Who did you help this week?_
- No one
_Who helped you this week?_
- Andrew
_What did you achieve last week?_
- Created a docekrfile for building a docker image
- Pipeline testing
- Created a snpEff database
_What would you like to work on this week?_
- Running docker
- Getting access rights to files
- Building docker image
_Where do you need help?_
- Building docker image

**Alex Gashanja**
Who did you help this week?
- Non
Who helped you this week?_
- Non
What did you achieve last week?_
- Proposal submission
_What would you like to work on this week?_
- preliminary tasks before working on my objective 1
_Where do you need help?_
- To have a hpc account

**Gladys Rotich**
_Who did you help this week?_
- None

_Who helped you this week?_
- Andrew

What did you achieve last week?_
- Proposal corrections and submission

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Data analysis

**Eric Kariuki**
_Who helped you last week?_
- Dr. Caleb

_What did you achieve last week?_
- Corrections by the supervisors on the dissertation

_What did you struggle with?_
- N/A

_What will I work on this week?_
- My MSc. internship report
- Submission of my dissertation to the university
- Back to the lab for some unfinished experiments

**Caroline Kogei**
_Who helped you last week?_
- N/A

_What did you achieve last week?_
- Created a deep learning model
- Neural Networks and computer vision concepts

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Optimising our model
- Deep learning community meetup
- Identifying tick dataset

_Where do you need help?_
- N/A

**Collins Kigen**
_Who did you help this week?_
- NA

_Who helped you this week?_
- Dr. Caleb

_What did you achieve last week?_
- Made progress in the Dada2 pipelines
- Tried out more datasets on the nf-core pipeline

_What did you struggle with?_
- Obtaining data containing metadata
- Testing the various pipelines

_What would you like to work on this week?_
- Finish up on testing the pipelines
- Compare the results from Yosef's pipeline and the nf-core pipeline
- Start on the report

# December 14th 2021

## Hello & Check-in

1. JB Mugi
2. Ruth Nanjala
3. Caroline Kogei
4. Gladys Rotich
5. Nyasita Ondari
6. Nelly Wambui
7. Okeyo Allan
8. Collins Kigen
9. Joyce Wangari
10. Eric Kariuki

**JB Mugi**
#### Who did you help this week?

* N/A
#### Who helped you this week?

* Dr. Caleb
* Kennedy Senagi
* Nehemiah
* Ruth Nanjala

#### What did you achieve last week?

* Literature review for our mini project
* Python programming
* Completed a comprehensive introduction for our mini project
* Coming up with a template for our
* Code Review

#### What did you struggle with?

* Collecting sufficient image data required for our mini project

#### What would you like to work on this week?

* Review more literature related to our project
* Collect more data for the mini project
* Iplement some of the recommendations that we got from our mentors during last weeks code review
* Introduction to AWS AI & ML Scholarship program
* Python programming

#### Where do you need help

* N/A

**Ruth Nanjala**

_Who did you help this week?_
- Interns
- John

_Who helped you this week?_
- Dr. Yang Luo
- Mamana Mbiyavanga

_What did you achieve last week?_
- HLA typing using HLA-VBSEQ tool
- Working with the interns
- Meet up with supervisor - HLA Imputation project
- ABN meeting
- Breast cancer project
- Edited the H3ABionet chipimputation project Github repo
- Worked with John

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Breast cancer project
- HLA imputation project
- Meet up with the HLA typing meeting
- Working with the interns

_Where do you need help?_
- N/A

**Caroline Kogei**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Dr. Caleb
- Ruth
- Nehemiah
- Kennedy
- Ken

_What did you achieve last week?_
- Literature review
- AWS machine learning program
- Inbuilt applications in Keras
- Code Review

_What did you struggle with?_
- Creating a well curated database for our mini-project

_What would you like to work on this week?_
- Literature review
- Create a data pool for the mini-project
- Look into CNN Architectures

_Where do you need help?_
- N/A

**Okeyo Allan**
_Who did you help last week?_
- None

_Who helped you last week?_
- Ruth Nanjala
- Hebrew Simeon
- Rose Wanjiku

_What did you achieve last week?_
- Successfully tested 3 variant calling pipelines
- Conducted a weekly code review session
- Undertook a variant calling nextflow tutorial

_What did you struggle with last week?_
- Running the pipelines with our own datasets
- Acquiring datasets

_What would you like to work on this week?_
- Testing a couple more pipelines
- Run the previous pipelines with our own datasets

_Where do you need help?_
- We will be glad to reach out where need be.

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- Ruth Nanjala
_What did you achieve last week?_
- BOSS miniproject
- proposal ammendments
_What did you struggle with?_
- None
_What would you like to work on this week?_
- BOSS miniproject
- proposal ammendments and submission
_Where do you need help?_
- Accessing the project data

**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- BOSS miniproject
- proposal ammendments
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- BOSS miniproject
- proposal ammendments and submission
- Working on my second dataset
_Where do you need help?_
- N/A

**Nelly Wambui**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Yosef Hamba
- Nehemiah Ongeso
- Ruth Nanjala
- Dr. Caleb Kibet
- Nabwire Asatsa

_What did you achieve last week?_
- Obtaining dataset and testing pipelines for our miniproject

_What did you struggle with?_
- Making adjustments to the 16S-Accreditation pipelines
- My short course

_What would you like to work on this week?_
- Progressing in our miniproject
- Making progress in my short course

_Where do you need help?_
- Miniproject

**Joyce Wangari**
_Who did you help this week?_
- No one
_Who helped you this week?_
- Ruth Nanjala
- Simeon Hebrew
- Rose Wambui
_What did you achieve last week?_
- reviewed existing pipelines managed to run 3 pipelines successfully
- Reviewed python questions
_What did you struggle with?_
- Running the pipelines with our test data
_What would you like to work on this week?_
- continue testing the pipelines
- review some python questions
_Where do you need help?_
- Running the pipelines with our test data

**Collins Kigen**
#### Who did you help this week?

NA

#### Who helped you this week?

* Dr. Caleb Kibet
* Ruth Nanjala
* Nehemiah

#### What did you achieve last week?

*

#### What did you struggle with?

* Running h3abionet 16s pipeline

#### What would you like to work on this week?

* miniproject
* Journal club presentation

#### Where do you need help

NA

**Eric Kariuki**

#### Who helped you this week?

### What did you achieve last week?
- Completed my thesis and worked on corrections

#### What would you like to work on this week?
- Work on corrections from other supervisors
- Prepare my intent to submit
- Meeting with my supervisors
- Carpentries training workshop

#### Who did you help this week?

* Replace this text with a one/two sentence description of who you helped this week and how.

#### Who helped you this week?

* Replace this text with a one/two sentence description of who helped you this week and how.

#### What did you achieve last week?

* Replace this text with a bullet point list of what you achieved last week.
* It's ok if your list is only one bullet point long!

#### What did you struggle with?

* Replace this text with a bullet point list of where you struggled last week.
* It's ok if your list is only one bullet point long!

#### What would you like to work on this week?

* Replace this text with a bullet point list of what you would like to work on next week.
* It's ok if your list is only one bullet point long!

#### Where do you need help

* Replace this text with a bullet point list of what you need help.
* It's ok if your list is only one bullet point long!
# December 6th 2021

## Hello & Check-in

1. Gladys Rotich
2. Ken Mugambi
3. Nyasita Ondari
4. Ruth Nanjala
5. Joyce Wangari
6. Nell\y Wambui
7. Okeyo Allan
8. Collins Kigen
9. Alex Gashanja
10. Caroline Kogei
11. JB Mugi
12. Eric Kariuki

**Gladys Rotich**
_Who did you help this week?_
- None
_Who helped you this week?_
- None
_What did you achieve last week?_
- BOSS miniproject
- proposal writing
_What did you struggle with?_
- None
_What would you like to work on this week?_
- BOSS miniproject
- proposal corrections
_Where do you need help?_
- Accessing the project data

**Ken Mugambi**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Nanopore - library prep
- BOSS miniproject
- Proposal writing
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- BOSS Miniproject
- Proposal amendments
- Interns miniprojects
- Interns python review
**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Submitted the first draft of my 1st objective results
- BOSS miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Proposal ammendments and submission
- BOSS miniproject

**Joyce Wangari**
Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Introduced to our mini-project
- Worked on some python problems
- Project presentation
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Start assessing the the different variant calling pipelines
_Where do you need help?_
- Mini-project
- python questions

**Okeyo Allan**
_Updates_
_Who did you help this week?_
- None
_Who helped you last week?_
- None
_WHat did you achieve last week?_
- Managed to come up with a work plan for our mini-project
- Shared the work plan with a pannel
- Journal club presentation
_What did you struggle with last week?_
- None
_Where do you need help?_
- Python practice questions
- Variant call pipelines

**Ruth Nanjala**
Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Meeting with the interns
- HLA typing

_What did you struggle with?_
- HLA typing using the HLAminer software

_What would you like to work on this week?_
- Working with the interns
- ABN meeting
- Meet with my supervisor to discuss on the manuscript writeup

_Where do you need help?_
- N/A

**Nelly Wambui**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Yosef Hamba
- Nehemiah Ongeso
- Ruth Nanjala
- Dr. Caleb Kibet

_What did you achieve last week?_
- Familiarizing with our mini-project
- Code review in which we presented our roadmap

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Going through challenging python questions
- Test existing 16srRNA pipelines and noticing any gaps

_Where do you need help?_
- Mini-project

**Collins Kigen**
#### Who did you help this week?

NA

#### Who helped you this week?

* Yosef Hamba
* Nehemiah Ongeso
* Ruth Nanjala
* Andrew
* Dr. Caleb Kibet

#### What did you achieve last week?

* Started 16s rRNA project
* Presented Roadmap for miniproject

#### What did you struggle with?
NA

#### What would you like to work on this week?

* Reviewing python assignments
* Miniproject

#### Where do you need help
NA

**Alex Gashanja**
_Who did you help this week?_
- None
_Who helped you this week?_
- Dr. Kibet
_What did you achieve last week?_
- First draft of research proposal
- BOSS meeting
_What did you struggle with?_
- Developing my methodology
_What would you like to work on this week?_
- Revise my proposal
- BOSS mini-project
_Where do you need help?_
- None
-

**Caroline Kogei**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Ken Murithi
- Andrew Espira

_What did you achieve last week?_
- Outlined the mini-project's workflow
- Project presentation
- Introduction to Deep Learning

_What did you struggle with?_
- Deep learning algorithms
- Applying filters to a vcf file

_What would you like to work on this week?_
- To find a research question to work around the project
- Identify a dataset that answers our research question
- Learn various machine learning algorithms

_Where do you need help?_
- Guidelines on the mini-project

**JB Mugi**

#### Who did you help this week?

* N/A

#### Who helped you this week?

* Dr. Caleb
* Andrew
* Ken
#### What did you achieve last week?

* Familiarise myself with the mini project that I will be taking for the next 2 months
* Coming up with a roadmap for the mini project
* A better understanding of VCF file manipulation and pseudogenome construction

#### What did you struggle with?

* Pseudogenome construction

#### What would you like to work on this week?

* Review algorithms that we can use in our mini-project
* Review available datasets on our mini-project
* Come up with a research question for our mini-project
* Review challenging python questions with Ken

#### Where do you need help

* Guidance on the best approach to take on the mini project

**Eric Kariuki**
_Who helped you this past week?_

_What did you struggle with?_
- The last objective of my research

_What did you achieve last week?_
- I got a few chapters of my thesis done
- Workaround to my last research objective

_Where do you need help?_
- Thesis review from my supervisors

# November 29th 2021

## Hello & Check-in
1. Ruth Nanjala
2. Eric Kariuki
3. Nyasita Ondari
4. Ken Mugambi
5. Joyce Wangari
6. Nelly Wambui
7. Okeyo Allan
8. Karega Pauline
9. Gladys Rotich
10. Collins Kigen
11. Caroline Kogei
## Updates

**Ruth Nanjala**
_Who did you help this week?_
- Interns
- PhD student
- Eric Kariuki

_Who helped you this week?_
- N/A

_What did you achieve last week?_
- Attended the EMBL Cancer Genomics conference
- Bioinformatics strategic meeting
- Interns code review
- Assisted a ugandan PhD student on the project he's working on
- HLA typing using the HLAreporter tool

_What did you struggle with?_
- HLAreporter tool

_What would you like to work on this week?_
- Introduce the interns miniprojects
- Work on another HLA typing tool
- Work with the PhD student

_Where do you need help?_
- N/A

**Eric Kariuki**
_What did you achieve last week?_
- Chapter 3 of my thesis
- Presented my research progress to the university department
- Bioinformatics unit strategic meeting
- ONT 16S data analysis pipeline with Oscar and John
- Reviewed the first two sections of a colleague's manuscript

_Who helped you this last week?_
- Ruth Nanjala
-
_What did you struggle with?_
- The last objective of my research
_What would you like to work on this week?_
- Thesis writing
- Review the last 2 sections of a colleague's manuscript
- Discuss the particulars of the ONT 16S Analysis pipeline
- Prepare for a presentation I have next week
_Where do you need help?_

**Nyasita Ondari**
_Who did you help this week?_
- N/A

_Who helped you this week?_
- Eric helped me interpret some of my results for objective

_What did you achieve last week?_
- Started reporting on the results for my first objective

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Objective one results and report writing
- BOSS miniproject: plant genome
- Proposal ammendment

**Ken Mugambi**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Caleb Kibet
_What did you achieve last week?_
- Proposal writing
_What did you struggle with?_
- Machine learning part of proposal writing
_What would you like to work on this week?_
- Nanopore sequencing
- Proposal writing
- BOSS miniproject: Plant genome
- Data analysis

**Gladys Rotich**
_Who did you help this week?_
- Bioinformatics student
_who helped you this week?_
- Andrew
_what did you achieve last week?_
- proposal writing
_What did you struggle with?_
- None
_what you like to work on this week?_
- proposal writing
- BOSS miniproject: viral analysis
- data analysis

**Okeyo Allan**
_Who did you help this week?_
- No one
_Who helped you this week?_
- Pauline Karega
_What did you achive this week?_
- Managed to run an analysis using Beast
_What did you struggle with this week?_
- Singling out sequences of interest
_What you want to work on this week_
- Introduction to mini-project
- Journal club presentations

**Joyce Wangari**
_Who did you help this week?_
- no one

_Who helped you this week?_
- Pauline

_What did you achieve last week?_
- Learnt data science and machine learning
- Working on our paper and code reviews

_What did you struggle with?_
- Retrieving the sequences of interest

_What you like to work on this week?_
- Introduction to our mini-projects
- Work on some python problems
- Finish up on the reproducible paper.

**Caroline Kogei**
_Who did you help this week?_
- No one

_Who helped you this week?_
- Eric Kariuki
- Dr. Caleb Kibet

_What did you achieve last week?_
- I had an introduction to Machine Learning and Data Science
- Reproducing a phylogenetics and phenotypic Research paper and understanding VCF file format

_What did you struggle with?_
- We had a challenge coming up with a pseudo - genome to create a phylogenetic tree

_what you like to work on this week?_
- Create a script that will pass filters to a VCF file and create a pseudo - genome
- Introduction to the mini-project

_Where do you need help?_
- Creating a script that will produce a pseudo genome for phylogenetic analysis

**Nelly Wambui**
_Who did you help this week?_
- No one.

_Who helped you this week?_
- Ruth helped us in our nextflow script and we made progress.

_What did you achieve last week?_
- Code review for our paper.
- Got to understand machine learning and data science more.
- We did our mini project and were able to do much of it and also started on our nextflow script for the mini project.

_What did you struggle with?_
- The mini project nextflow script.

_What would you like to work on this week?_
- Continue with the nextflow script and hopefully be able to help and learn from my colleagues.
- Go through the python assignment we had a while back.

_Where do you need help?_
- Not needing help yet but where I face challenges I sure will ask. Thanks in advance.

**JB Mugi**

#### Who did you help this week?

* N/A

#### Who helped you this week?

* Eric Kariuki helped with understanding VCF and filters applied during variant calling
* Dr. Caleb advised us on how to go about solving a problem when you can't find a ready-made tool.

#### What did you achieve last week?

* Refining the scripts that we had previously used in our paper reproduction pipelines.

#### What did you struggle with?

* Finding tools to construct a pseudogene by substituting base calls (variant or non-variant) on a reference genome.

#### What would you like to work on this week?

* Come up with a script to construct a pseudogene
* Start on the mini-project.

#### Where do you need help

* Coming up with a sript to construct a pseudogene

#### Karega Pauline
#### Who did you help this week?

* Joyce and Allan

#### Who helped you this week?

* My supervisors

#### What did you achieve last week?

* I managed to get duplications and losses for my genes along with expansion and contraction rates
* I got the CAFE protocol working for me

#### What did you struggle with?

* The CAFE protocol
* BEAST analysis for my work

#### What would you like to work on this week?

* BEAST analysis to date my trees
* Get dN/dS ratios
* Kick off the BOSS mini projects

#### Where do you need help

* Visualization of my results

**Collins Kigen**
#### Who did you help this week?

* N/A

#### Who helped you this week?

* Ruth

#### What did you achieve last week?

* Presentation for code review

#### What did you struggle with?

* I had a chalenge in getting the nextflow to resume execution of processs rather tha re running from the start

#### What would you like to work on this week?

* 2nd Miniproject
* Complete automation of the pipelines for first miniproject using nextflow

#### Where do you need help

* Advanced concepts in nextflow