---
# System prepended metadata

title: Bioinformatics Team Meetings from April 2022

---

# Bioinformatics Team Meetings from April 2022

[Previous Check ins - March 2021](https://hackmd.io/-DXVadqmQuuh7F3g_M_6JQ) and [Previous Check ins - November 2021](https://hackmd.io/1Jh94XV-SKOWRKzJex5Qxg) and [March 2022](https://hackmd.io/@calkibet/BJYVAAQLF)


[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

_What did you achieve last week?_

_Who did you help last week?_

_Who helped you last week?_

_What did you struggle with?_

_What would you like to work on this week?_

_Where do you need help?_

## Hello & check in 
## 28th November 2022

1. Samuel Mwasya.
2. Vanessa Natasha
3. Bonface Onyango
4. Jimmy Nkaiwuatei

**Samuel Mwasya**
_What did you achieve last week?_
- Writing final report.

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

_Who helped you last week?_
- N/A

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Final report and manuscript writing.

_Where do you need help?_
- N/A


**Vanessa Natasha**
 _What did you achieve last week?_
 - Completed differential abundance analysis (DAA) for both Archaea and Bacteria

_Who did you help last week?_
 - N/A
 
_Who helped you last week?_
 - Nehemiah
 
_What did you struggle with?_
 - N/A
 
_What would you like to work on this week?_

 - Preparing slides for the final presentation
 - Report compiling and writing
 
_Where do you need help?_
 - N/A

**Bonface Onyango**
_What did you achieve last week?_
- Conceptual and logical design of the database
- Continued with state of the art literature review

_Who did you help last week?_
- N/A
_Who helped you last week?
- Mandela

_What did you struggle with?_
- Implementing search functionality

_What would you like to work on this week?_
- Explore on methods and tools
- KEMRI data re-use codeathon
- Prototype website imlemantation

_Where do you need help?_
- N/A

**Jimmy Nkaiwuatei

_What did you achieve last week?_
- fungal abundance calculation and plotting for bee metagenomics analysis.
- report writing.
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Anne
_What did you struggle with?_
- instalation of Cairo package.
- removal of unclassified species(NAs) prior to plotting.
_What would you like to work on this week?_
- beta and alpgha diveristy plotting.
- report writing.
_Where do you need help?_
- removal of the NAs in the taxa.
 
## Hello & check in 
## 21st November 2022
1. Vanessa Natasha
2. Nehemiah Ongeso
3. Fredrick Kebaso
4. Cynthia Kamau
5. Mark Njama
6. Jimmy Nkaiwuatei


**Vanessa Natasha**
 _What did you achieve last week?_
 - Completed differential abundance analysis (DAA) for Archaea

_Who did you help last week?_
 - N/A
 
_Who helped you last week?_
 - Nehemiah
 
_What did you struggle with?_
 - N/A
 
_What would you like to work on this week?_

 - Complete DAA for the other microbes
 - Report compiling and writing
 
_Where do you need help?_
 - N/A


**Nehemiah Ongeso**

_What did you achieve last week?_
- Responding to reviwers and clarifying tools methods used to analyze microbe occurence.

_Who did you help last week?_

_Who helped you last week?_

_What did you struggle with?_

_What would you like to work on this week?_
- Review of manuscript drafts (soil, rumen,bees, hpc)

_Where do you need help?_


**Cynthia Kamau**

_What did you achieve last week?_

*  Decluttering the HPC
*  Working on the HPC Manuscript

_Who did you help last week?_

* N/A

_Who helped you last week?_

* Nehemiah
* Dr. Caleb

_What did you struggle with?_

*  N/A

_What would you like to work on this week?_

* Finish cleaning the HPC
* Work on the HPC Manuscript

_Where do you need help?_

* N/A

**Fredrick Kebaso**

_What did you achieve last week?_
- Assembly of *H.variegata* sequences 
- Proposal writting
_Who did you help last week?_
- N/A

_Who helped you last week?_
- Nehemiah
_What did you struggle with?_
- CHPC Server

_What would you like to work on this week?_
- Finding consensus assembly

_Where do you need help?_
- N/A

**Mark Njama**
_What did you achieve last week?_
- made some progress on writing the report for tick metagenomics
- found more comparisions between the pipelines


_Who did you help last week?_
- Ann Laigong'
- Jimmy

_Who helped you last week?_
- Nehemiah Ongeso
- Ann Laigong

_What did you struggle with?_
- creating a count matrix for my reads still working on that 

_What would you like to work on this week?_
- complete the write up for the  usability and overall performance of the two pipelines

_Where do you need help?_
- creating a count matrix for the reads in tick metagenomics

**Jimmy Nkaiwuatei

_What did you achieve last week?_
- nf-core ambliseq analysis for bee metagenomic analysis.
- project report writing.
_Who did you help last week?_
 - N/A
_Who helped you last week?_
- Nehemiah and Anne
_What did you struggle with?_
- plotting of abundance and diversity
_What would you like to work on this week?_
- report writing
- plotting of abundance and diversity
_Where do you need help?














## Hello & check in 
## 14th November 2022
1. Ken Mugambi
2. Ann Laigong'
3. Samuel Mwasya 
4. Vanessa Natasha
5. Fredrick Kebaso
6. Declan Joseph
7. Bonface Onayngo


**Ken Mugambi**

_What did you achieve last week?_

- Thesis writing and corrections
- Self learning

_Who did you help last week?_

- Fellow colleagues

_Who helped you last week?_

- Fellow colleagues
- Thesis supervisors

_What did you struggle with?_

- N/A

_What would you like to work on this week?_

- Repo

_Where do you need help?_

- Haven't encountered any.

**Ann Laigong'**

_What did you achieve last week?_

- Completed abundance analysis and generated graphs using the updated metadata.
- Made progress with the report writing.

_Who did you help last week?_

- N/A

_Who helped you last week?_

- Nehemiah Ongeso

_What did you struggle with?_

- N/A

_What would you like to work on this week?_

- Proceed with writing the report.

_Where do you need help?_

- Haven't encountered any but will reach out should I need assistance.

**Samuel Mwasya**

_What did you achieve last week?_
- Report writting and fine tuning of the project results.

_Who did you help last week?_
- Fellow colleagues.

_Who helped you last week?_
- Fellow colleagues.
- Nehemiah Ongeso.

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Proceed with developing manuscript.

_Where do you need help?_
- N/A



**Vanessa Natasha**
 _What did you achieve last week?_
 - Completed functional analysis

_Who did you help last week?_
 - Jimmy
 
_Who helped you last week?_
 - Nehemiah
 
_What did you struggle with?_
 - N/A
 
_What would you like to work on this week?_
 - Differential protein expression analysis
 - Report compiling and writing
 
_Where do you need help?_
 - N/A

**Fredrick Kebaso**

_What did you achieve last week?_

- Cleaned my data 
- Proposal writting

_Who did you help last week?_

- N/A

_Who helped you last week?_

- Nehemiah

_What did you struggle with?_

- Computattinal resources

_What would you like to work on this week?_

- Proposal writting
- Assembly of *H.variegata*
- Develop project workflow 

_Where do you need help?_

- Chpc


**Nehemiah Ongeso**
_What did you achieve last week?_


_Who did you help last week?_

_Who helped you last week?_

_What did you struggle with?_

_What would you like to work on this week?_

- Responding to reviewers comments
- Interaction network and functional analysis of metagenomic data
- Soil metagenomic analyis (16s & ITS)

_Where do you need help?_

**Declan Joseph**

_What did you achieve last week?_

- Setting up the sample management system locally using container ochestration (Kubernetes)
- Looking into how to implement authentication and notifications in a web application.

_Who did you help last week?_
n/a
_Who helped you last week?_
n/a
_What did you struggle with?_

- understanding how authentication and notifications work using firebase.
- Setting up postgres database on Kubernetes using StatefulSet and persistent volumes.

_What would you like to work on this week?_

- Setup postgres database using bitnami's helm chart so as to enable replication.
- Look into how to secure containerized applications.
- utilize firebase admin sdk to send notifications to a test client web applications.
- Update UI on test client web application when a notification is received.

_Where do you need help?_
n/a

**Bonface Onyango**
_What did you achieve last week?_
- Wrote proposal literature review
- Explored advanced functionality of nextjs

_Who did you help last week?_
- Pauline

_Who helped you last week?_
- Dr. Caleb, Violet,Dr. Kennedy,Dr. Copeland,Salvado

_What did you struggle with?_
- N/A

_What would you like to work on this week?
- Polish on literature review based on supervisor's comment
- Database normalization

_Where do you need help?_
- N/A

## Hello & check in 
## 07th November 2022
1. Samuel Mwasya
2. Vanessa Natasha
3. Fredrick Kebaso
4. Nehemiah Ongeso
5. Bonface Onyango
6. Jimmy NKaiwuatei
7. Ann Laigong'
**Samuel Mwasya**

_What did you achieve last week?_

- Fine tuned my results from the project.
- Merging of metagenome study visualization.

_Who did you help last week?_

- Fellow colleagues.

_Who helped you last week?_

- Nehemiah Ongeso.

_What did you struggle with?_

- N/A

_What would you like to work on this week?_

- Report writing in regards to the metagenome project.

_Where do you need help?_

- Haven't encountered any.



**Vanessa Natasha**
 _What did you achieve last week?_
 - Completed diversity analysis

_Who did you help last week?_
 - Jimmy
 
_Who helped you last week?_
 - Nehemiah
 
_What did you struggle with?_
 - N/A
 
_What would you like to work on this week?_
 - Functional analysis 
 - Report compiling and writing
 
_Where do you need help?_
 - N/A

**Fredrick Kebaso**

_What did you achieve last week?_

- Proposal writting - Literature search

_Who did you help last week?_

- N/A
- 
_Who helped you last week?_
- N/A

_What did you struggle with?_


_What would you like to work on this week?_

_Where do you need help?_


**Nehemiah Ongeso**

_What did you achieve last week?_
- Analysis of 16s and ITS soil data

_Who did you help last week?_
- Pauline and Jalloh

_Who helped you last week?_

_What did you struggle with?_

_What would you like to work on this week?_
- Prepare for the science journey webinar (18th November, 2022): Making Poster & Mailing Speakers
- Writing and reviewing of the (bee and livestock rumen) manuscripts.
- Optimizing result visualizations and outputs (jpeg, png, svg, tiff, and pdf formats)
- Output functional analysis results using STUMP 

_Where do you need help?_
- Creating Science Journey webinar poster

**Bonface Onyango**
_What did you achieve last week?_
- Literature search on Biodiversity website tools and technologies
- Learning about nextjs data fetching from database

_Who did you help last week?_

- Violet, Cynthia

_Who helped you last week?_

- Joseph, Laura

_What did you struggle with?_

- Understanding data fetching concepts in Nextjs

_What would you like to work on this week?_

- Data modeling 
- Website System design methos

_Where do you need help?_

- N/A

**Jimmy Nkaiwuatei

_What did you achieve last week?_
- Taxonomic classification
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Natasha
_What did you struggle with?_
- constructing a phyloseq object
_What would you like to work on this week?_
- construct and analyze a phyloseq object
_Where do you need help?_
- installing dada2 in Rstudio cloud

**Ann Laigong**

_What did you achieve last week?_

- I began working on the manuscript for the bee metagenomic analysis.
- Generated all the abundance plots for the different variables.

_Who did you help last week?_

- N/A.

_Who helped you last week?_

- Nehemiah Ongeso.

_What did you struggle with?_

- N/A

_What would you like to work on this week?_

- Proceed with writing the manuscript.

_Where do you need help?_

- N/A.

## Hello & check in 
## 31st October 2022
1. Samuel Mwasya
2. Vanessa Natasha
3. Ann Laigong'
4. Fredrick Kebaso
5. Jimmy Nkaiwuatei
6. Declan Joseph
7. Bonface Onyango

**Samuel Mwasya**

_What did you achieve last week?_

- Fine tuning statical analysis (Alpha,beta) of the microbiome project.

_Who did you help last week?_

- Fellow colleagues.

_Who helped you last week?_

- Nehemiah Ongeso.

_What did you struggle with?_

- N/A

_What would you like to work on this week?_

- Report writing.

_Where do you need help?_

- N/A

 
 
**Vanessa Natasha**
 _What did you achieve last week?_
 - Finished diversity analysis for fungi and Protozoa with nf-core and Dada2

_Who did you help last week?_
 - Jimmy
 
_Who helped you last week?_
 - Nehemiah
 
_What did you struggle with?_
 - N/A
 
_What would you like to work on this week?_
 - Functional analysis 
 - Report compiling and writing
 
_Where do you need help?_
 - N/A

**Ann Laigong'**

_What did you achieve last week?_
 - Completed abundance analysis and alpha diversity

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

_Who helped you last week?_
- Nehemiah

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Beta Diversity

_Where do you need help?_
- N/A

**Fredrick Kebaso**

_What did you achieve last week?_

- Identified existing gaps in the Hippoboscus research work
- Formulated my research question

_Who did you help last week?_
- N/A
_Who helped you last week?_
- Bonface

_What did you struggle with?_
N/A

_What would you like to work on this week?_
- Continue with literature search
- Proposal writing

_Where do you need help?_
- N/A

**Jimmy Nkaiwuatei**

_What did you achieve last week?_
- Filtration and trimming of Bee metagenomic data  
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Natasha
- Samwel
- Nehemiah
_What did you struggle with?_
- taxonomic classification of the sequences
_What would you like to work on this week?_
- Constructing a phyloseq
- visualization of results
_Where do you need help?_
- N/A

**Declan Joseph**
_What did you achieve last week?_
- Research in deployment of systems in the cloud using docker and kubernetes.

_Who did you help last week?_
- N/a

_Who helped you last week?_
- N/a

_What did you struggle with?_
- N/a

_What would you like to work on this week?_
- Create a local deployment of the sample management system using container ochestration.

_Where do you need help?_
- N/a

**Bonface Onyango**

_What did you achieve last week?_
- Exploring on Nextjs file structure and organisation
- Dynamic routing in Nextjs 
- Literature review on Biodiversity websites: functionality and  technologies used


_Who did you help last week?_
- Fredrick

_Who helped you last week?_
- Fredrick, Dr. Kennedy, Dr. Copeland,Joseph,Henry Kyalo

_What did you struggle with?_
- Most of the biodiversity websites have limited scholarly work in regards to their technologies

_What would you like to work on this week?_
- Continue with literature search on biodiversity websites:functionality,evaluation,deployment,technologies
- Image optimization in nextjs 
- Working on supervisor's comments

_Where do you need help?_
- N/A
## Hello & check in 
## 24th October 2022
1. Vanessa Natasha
2. Samuel Mwasya
3. Jimmy Nkaiwuatei
4. Cynthia Kamau
5. Ann Laigong'
6. Nehemiah Ongeso
7. Bonface Onyango


**Vanessa Natasha**

_What did you achieve last week?_
 - Finished diversity analysis for archaea and bacteria
 - Documented my diversity analysis
 
_Who did you help last week?_
 - Jimmy
 
_Who helped you last week?_
 - Nehemiah
 
_What did you struggle with?_
 - assigning taxa for protozoa
 
_What would you like to work on this week?_
 - Diversity analysis with Nf-core ampliseq
 - Report compiling and writing
 
_Where do you need help?_
 -N/A

**Samuel Mwasya**

_What did you achieve last week?_

- Writting a progress report.

_Who did you help last week?_

- Fellow interns
 
_Who helped you last week?_
- Dr. Kibet
- Nehemiah Ongeso
- Fellow interns


_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Final review of my project.

_Where do you need help?_
- N/A

**Jimmy Nkaiwuatei**

_What did you achieve last week?_
- microbiome analysis of the bee data using dada2
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Natasha and
- Nehemiah
_What did you struggle with?_
- taxonomic classification of the variant sequences.
_What would you like to work on this week?_
- Visualization of the dada2 bee data using phyloseq tool.
_Where do you need help?_
- installing phyloseq

**Cynthia Kamau**

_What did you achieve last week?_

Setting up user accounts for my HPC

_Who did you help last week?_

N/A

_Who helped you last week?_

* Dr. Caleb 
* Nehemiah
* Fellow interns


_What did you struggle with?_

Configuring Slurm accounting db

_What would you like to work on this week?_

* Finishing HPC configuration
* Start working on the HPC Manuscript

_Where do you need help?_

N/A

**Ann Laigong'**
What did you achieve last week?_
Pre-processing of Bee-Metagenomics data and abundance analysis

_Who did you help last week?_
N/A

_Who helped you last week?_
* Nehemiah

_What did you struggle with?_
Installing packages in R because of the R version and updating R and R studio

_What would you like to work on this week?_
BLAST of the sequences to characterize them to the species level
Use R to show similar and dissimilar species and genus in the different sampling sites

_Where do you need help?_
N/A

**Nehemiah Ongeso**
_What did you achieve last week?_
- Wrote a grant proposal.
- Soil microbiome analysis

_Who did you help last week?_
- Interns
- Msc Students

_Who helped you last week?_
- Dr. Caleb

_What did you struggle with?_
- Troubleshooting nextflow errors

_What would you like to work on this week?_
- Drafting analysis reports for Rumen and Bee tree microbiome.

_Where do you need help?_
- NA

**Bonface Onyano**
_What did you achieve last week?_
- Presented monthly progress report to the supervisors
- Literature review  on existing biodiversity websites
- Prototype database design and implementation

_Who did you help last week?_
- Fredrick

_Who helped you last week?_
- Joseph

_What did you struggle with?_
- Dynamic routing in web development

_What would you like to work on this week?_
- Work on supervisor comments regarding literature review
- Literature review  on website Tools 

_Where do you need help?_



## Hello & check in 
## 17th October 2022
1. Samuel Mwasya
2. Nehemiah Ongeso
3. Ken Mugambi
4. Vanessa Natasha
5. Fredrick Kebaso
6. Bonface Onyango
7. Jimmy Nkaiwuatei
8. Ann Laigong'

**Fredrick Kebaso**

What did you achieve last week?

- Trained on Epigenetics particularly on cassava
- Literature search on:
    1. Glossina genome
    2. Trypanosome (*T.congolense*) genome - *On going*

Who did you help last week?
 - N/A
Who helped you last week?
- Ken Mugambi
- Nehemiah Ongeso
- Gladys 


**Vanessa Natasha**
What did you achieve last week?
 - Started on the diversity analysis of our project

Who did you help last week?
 - N/A

Who helped you last week?
 - Nehemiah Ongeso
 - My fellow interns


 - Merging my reads in the DADA


What would you like to work on this week?
- finish on the diversity analysis for bacteria and archaea


Where do you need help?
- N/A

**Ken Mugambi**
_What did you achieve last week?_
- EMBNet workshop
- Thesis corrections
- Machine and deep learning reading
_Who did you help last week?_
- Kebaso
- Laurah
_Who helped you last week?_
- Nehemiah Ongeso
- Gladys
- Kebaso
- Dr.Caleb
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Finalising on project
- Continue reading
_Where do you need help?_
- N/A
- 
**Bonface Onyango**
_What did you achieve last week?_
- Literature review
- Tutorials on Postgres Database
- Web Technologies search 

_Who did you help last week?_
- Mark

_Who helped you last week?_

- Salvado, Joseph,Kebaso

_What did you struggle with?_
_ Some metadata files were missing

_What would you like to work on this week?_
_ Continue with literaure review
_ Continue with search on appropriate web technologies to use in the project
_ Continue with database design

_Where do you need help
_ N/A

**Samuel Mwasya**
_What did you achieve last week?_
- Worked on Gut microbiome project.
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Nehemiah Ongeso
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Finalising on project.
_Where do you need help?_
- N/A

**Nehemiah Ongeso**
_What did you achieve last week?_
- Epigenetics crash course
_Who did you help last week?_
- Interns
_Who helped you last week?_
- NA

_What did you struggle with?_
- NA

_What would you like to work on this week?_
- Help interns to visualize Microbiome results and start writing manuscript draft: Methods and Result section
- Manuscripts: Insect gut microbiome, PPN-Interaction
- Automate gene co-expression network analysis pipeline to nextflow.
- 

_Where do you need help?_
- Optimizing microbiome visualization

**Jimmy Nkaiwuatei
What did you achieve last week?_
- Generation of hitmaps for parasites using idseq tool.
- Preparation of contigs for the parasites.
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Mark
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Phylogenetic analysis of the parasites' contigs
_Where do you need help?_
- I will request for any help when stuck. 

**Ann Laigong**

What did you achieve last week?_
Perfoming alpha diversity analysis on a test sample for practice

_Who did you help last week?_
N/A

_Who helped you last week?_
Nehemiah

_What did you struggle with?_
Perfoming beta diversity analysis

_What would you like to work on this week?_
Perfoming alpha, beta and abundance analysis

_Where do you need help?_
N/A



## Hello & check in 
## 3rd October 2022
1. Samuel Mwasya
2. Vanessa Natasha
3. Nehemiah Ongeso
4. Ken Mugambi
5. Fredrick Kebaso
6. Bonface Onyango 
7. Mark Njama
8. Ann Laigong'

**Samuel Mwasya**
_What did you achieve last week?_
- Performed amplicon analysis using nf-core/ampliseq.

_Who did you help last week?_
- N/a

_Who helped you last week?_
- Dr. Caleb, Nehemiah Ongeso.

_What did you struggle with?_
- Qiime2 module in the ampliseq pipeline.

_What would you like to work on this week?_
- Downstream analysis of microbial community.

_Where do you need help?_
- Beta diversity and alpha diversity.

**Mark Njama**
_What did you achieve last week?_
- Manged to annotate some of our taxon on CZID
- Began doing our analysis on the HPC.
_Who did you help last week?_
- Jimmy and caught up Ann with the HPC
_Who helped you last week?_
- Natasha Vanessa with fastqc
_What did you struggle with?_
- Host filtration with STAR on the HPC
_What would you like to work on this week?_
- Finish annotation  of all our samples
- Carry out assemblies with geneious prime
 _Where do you need help?_
- N/A

**Vanessa Natasha**
_What did you achieve last week?_
- Finished quality control in the project
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Nehemiah
- Laurah
- Sam
- Ken
_What did you struggle with?_
- Using a for loop in cutadapt
_What would you like to work on this week?_
- Using DADA2 for data analysis
_Where do you need help?_
- I'm not sure yet

**Bonface Onyango**
_What did you achieve last week?_

- Obtained dataset files
- Inspection of the data files
- Started Literature review

_Who did you help last week?_
- Violet Chege

_Who helped you last week?_
- Dr. Copeland, Dr. Caleb, Fredrick Kebaso,Wilson

_What did you struggle with?_
- Referencing using Latex

_What would you like to work on this week?_
- Continue with data files inspection
- Database design
- ASBCB codeathon
_Where do you need help?_
- N/A

**Ann Laigong'**

What did you achieve last week?_
Running the nf-core/ampliseq pipeline on the Bee-Metagenomic data

_Who did you help last week?_
N/A

_Who helped you last week?_
Nehemiah
Dr.Caleb

_What did you struggle with?_
Perfoming Qiime2 on the ampliseq pipleine

_What would you like to work on this week?_
Visualization of the results using R

_Where do you need help?_
N/A


## Hello & check in 
## 26th september 2022
1. Ken Mugambi
2. Samuel Mwasya
3. Mark Njama
4. Vanessa Natasha
5. Jimmy NKaiwuatei
6. Cynthia Kamau
7. Ann Laigong'

**Cynthia Kamau**

_What did you achieve last week?_

* I managed to install the OS needed for my HPC server, and connect the desktops using IP addresses

_Who did you help last week?_

* N/A

_Who helped you last week?_

* Dr Caleb
* Fellow colleagues

_What did you struggle with?_

* Configuring my desktops to server nodes

_What would you like to work on this week?_

* Finish setting up my HPC
* Start running test workloads
* Document on HPC

_Where do you need help?_

* N/A

**Samuel Mwasya**

_What did you achieve last week?_

- Dry running the nf-core/ampliseq for diversity analysis. 

_Who did you help last week?_

- N/A
 
_Who helped you last week?_

- Ruth Nanjala 
- DR. Caleb

_What did you struggle with?_

- Configuring the errors in  nfcore/ampliseq pipeline. 

_What would you like to work on this week?_

- Diversity analysis using the assigned dataset for mini-project.

_Where do you need help?_

- N/A

**Mark Njama**
_What did you achieve last week?_
- Managed to complete the website pipeline used for tick metagenomics
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Dr. caleb ahd Nehemiah
_What did you struggle with?_
- Compiling a program on the HPC
_What would you like to work on this week?_
- Work closely with Jimmy to complete the viraldAI pipeline
_Where do you need help?_
- Compiling a specific program on the HPC 

**Ken mugambi**
-What did you achieve last week?_
Thesis writing
_Who did you help last week?_
N/A
_Who helped you last week?_
N/A
_What did you struggle with?_
N/A
_What would you like to work on this week?_
Thesis writing
_Where do you need help
n/a


**Vanessa Natasha**
-What did you achieve last week?_
Got the data of our project did a Quality control
_Who did you help last week?_
N/A
_Who helped you last week?_
N/A
_What did you struggle with?_
Getting a pipeline for functional analysis
_What would you like to work on this week?_
Using cutadapt,DADA2 and Barrnap
_Where do you need help
n/a

**Jimmy Nkaiwuatei**
_What did you achieve last week?_
Quality analysis of tick samples using IDseq
geneartion of the VRLDAI workflow
_Who did you help last week?_
 N/A
_Who helped you last week?_
Mark
_What did you struggle with?_
generating the pipeline for viralsearch tool.
_What would you like to work on this week?_
execution of the VLRDAI pipeline
_Where do you need help?_
i will reach out for help when stuck.

**Ann Laigong'**

_What did you achieve last week?_

N/A

_Who did you help last week?_

N/A

_Who helped you last week?_

N/A

_What did you struggle with?_

N/A

_What would you like to work on this week?_

Alternative pipelines for metagenomic pathogen detection and comparison of the results.

_Where do you need help?_

N/A


## 19th September 2022
1. Samuel Mwasya
2. Jimmy Nkaiwuatei
3. Mark Njama
4. Ann Laigong'

**Samuel Mwasya**
_What did you achieve last week?_

- Generated a workplan for main mini-project.
- Did a code review.

_Who did you help last week?_

- None

_Who helped you last week?_

- None

_What did you struggle with?_

- None

_What would you like to work on this week?_

- Start working on main mini-project.

_Where do you need help?_

- Basic knowledge of the hpc.

**Jimmy Nkaiwuatei

_What did you achieve last week?_
generation of IDseq pipeline
_Who did you help last week?_
N/A
_Who helped you last week?_
N/A
_What did you struggle with?_
N/A
_What would you like to work on this week?_
Implementation of the idseq pipeline
_Where do you need help?_
I wil reach out when stuck

**Mark Njama**
_What did you achieve last week?_
- Downloaded our sequences from IDseq
_Who did you help last week?_
- N/A
_Who helped you last week?_
- N/A
_What did you struggle with?_
- formatting of our metadata for upload to IDseq
_What would you like to work on this week?_
- Going through the website pipleline used for tick-metagenomics
_Where do you need help?_
- N/A

**Ann Laigong'**
_What did you achieve last week?_

Retrieval of sequences from CZ-ID 
Started using CZ-ID utilising miniwdl


_Who did you help last week?_

N/A

_Who helped you last week?_

N/A

_What did you struggle with?_

Building a docker image for the tools required for the cz-id pipelines

_What would you like to work on this week?_

Building the docker image for cz-id on docker hub
Alternative pipelines for metagenomic pathogen detection and comparison of the results.

_Where do you need help?_

N/A


## Hello & check in 
## 5th September 2022
1. Ruth Nanjala
2. Mark Njama
3. Vanessa Natasha
4. Cynthia Kamau
5. Ann Laigong
6. Jimmy Nkaiwuatei

**Cynthia Kamau**
_What did you achieve last week?_
- Finished up on the 100 Python challenge questions
- Learnt how to use Rmarkdown scripts for documentation
- Did a successful phylogenomic analysis for our mini-project 

_Who did you help last week?_
N/A

_Who helped you last week?_
- Ruth
- Ken
- Pauline
_What did you struggle with?_
- Using any programming language assignment
- Understanding Snakemake

_What would you like to work on this week?_
- Data science and ML
- Mini-project
- Snakemake
_Where do you need help?_
- No.3 of the Use any programming language assignment

**Mark Njama**
_What did you achieve last week?
- Finalized on the WNV paper and created slides on the same
- created an Rmarkdown script for the advanced R questions
_Who did you help last week?_
- Ann Laigong
- Vanessa Natasha
_Who helped you last week?_
- Vanessa Natasha
- Pauline Karega
- Ruth Nanjala
_What did you struggle with?_
- using any programming language
- KaKs calculator
_What would you like to work on this week?_
- looking forward to machine learning
_Where do you need help?_
- coding exercise using any language(number 3)

**Vanessa Natasha**
_What did you achieve last week?_
- Made a workplan for the project

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

_Who helped you last week?_
- N/A

_What did you struggle with?_
- Functional analysis
- understanding the nf- core pipeline

_What would you like to work on this week?_
- Functional analysis
- Machine-learning
- running the nf-core pipeline
-
_Where do you need help?_
- N/A

**Ruth Nanjala**
_What did you achieve last week?
- Interns code review
- Interns presentations
- Imputation manuscript
- Reports writing
_Who did you help last week?_
- Interns
_Who helped you last week?_
- N/A
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Interns mini-projects presentations
- Assigning mini-projects to interns
_Where do you need help?_
- N/A

**Ann Laigong**

_What did you achieve last week?_ 

My patner and I manage dto perfom analysis using BEAST.
I managed to complete most of my assignments.
My first solo presentation

_Who did you help last week?_

N/A

_Who helped you last week?_
* Vanessa
* Cynthia
* Ruth

_What did you struggle with?_
* Snakemake
* Python scripting

_What would you like to work on this week?_
* Python scripts
* The reproducing a paper presentation

_Where do you need help?_
* Python scripting

** Jimmy Nkaiwuatei**

_What did you achieve last week?_
* completed python scripting questions
* Bash scripting exercise
* Advance reading on R programming
_Who did you help last week?_
* I did not help anyone last week
_Who helped you last week?_
* Mark
_What did you struggle with?_
* Python scripting questios
* Bash scripting exercise
_What would you like to work on this week?_
* mini  project workflow generation
_Where do you need help?_
* I still need a little help on bash scripting

## Hello & check in
## 29th August 2022
1. Ann Laigong
2. Vanessa Natasha
3. Samuel Mwasya
4. Nyasita Ondari
5. Cynthia Kamau
6. Mark Njama
7. Jimmy Nkaiwuatei

**Vanessa Natasha**
_What did you achieve last week?_
- I managed to do bayesian phylogenies with Mr Bayes

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

_Who helped you last week?_
- Pauline
- Ruth
- Mark
-

_What did you struggle with?_
- Bayesian phylogenies with BEAST
- Raxml 
- Tree annotator on BEAST

_What would you like to work on this week?_
- Python scripting
- Snake make
- Finish mini project
- Finish any coding language questions
-
_Where do you need help?_
- python


**Ann Laigong**   

What did you achieve last week?_  
Generation of MCMC trees using MrBayes in CIPRES  

_Who did you help last week?_
N/A  

_Who helped you last week?_
* Ruth Nanjala  
* Pauline Karega  
* Samuel Mwasya  
* Cynthia Kamau  

_What did you struggle with?_
* BEAST and MrBayes on the command line  
* Using Tracer and Tree Annotator  

_What would you like to work on this week?_
* RaxML and PAML on the command line  
* BEAST and MrBayes on the command line  

_Where do you need help?_
* Python  



**Samuel Mwasya**
_What did you achieve last week?_
- Created a local blast database.
_Who did you help last week?_
- Ann Laigong
_Who helped you last week?_
- Ruth Nanjala
- Pauline Karega
_What did you struggle with?_
- Blasting on local blast database
_What would you like to work on this week?_
- Finalizing on the mini-project
_Where do you need help?_
- How to set an e value for blasting large sequences to capture the highest to capture specified hit score


**Cynthia Kamau**
_What did you achieve last week?_
- Created a local BLAST database for our mini-project
_Who did you help last week?_
- N/A
_Who helped you last week?_
- Ruth Nanjala
- Pauline Karega
_What did you struggle with?_
- Using Blast on the command line
_What would you like to work on this week?_
- Finishing up on the mini-project and assignments
_Where do you need help?_
- Blasting large sequences on the command line

**Mark Njama**
_What did you achieve last week?_
- made some progress with the replication of the WNV paper
_Who did you help last week?_
- Vanessa Natasha
- Jimmy Nkaiwuatei
_Who helped you last week?
- Ruth Nanjala
- Pauline Karega
- Samuel Mwasya
_What did you struggle with?_
- replicating the paper specifically the augur application
_What would you like to work on this week?_
- finishing up the python questions 
_Where do you need help?_
- I need help with the WNV paper trying to find a solution for error with the ```augur filter``` command.
 
 ** Jimmy Nkaiwuatei
 _What did you achieve last week?_
* Phylogenetic analysis
* Python scripting
_Who did you help last week?_
* N/A
_Who helped you last week?_
* N/A
_What did you struggle with?_
* Python scripting.
_What would you like to work on this week?_
* Synonymous and non-synonymous ratio calculation.
* Phylogenetic tree generation
* Snakemake 
_Where do you need help?_
## Hello & check in
## 6th June 2022
1. Ruth Nanjala
2. Gladys Rotich
3. Rodney Omukuti
4. Alex


**Ruth Nanjala**
_What did you achieve last week?_
- Attending and presenting a talk the 19th H3Africa meeting

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

_Who helped you last week?_
- N/A

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Attending and presenting a talk at the ACE Bioinformatics Symposium in Mali
- Internship manuscript
- Internship report
- Imputation analysis
- Imputation manuscript

_Where do you need help?_
- N/A


**Gladys Rotich**
_What did you achieve last week?_
- Worked on objective 2
- Writing report on what I have gotten so far
- met my supervisors
_Who did you help last week?_
- None
_Who helped you last week?_
- Quirine helped me ammend my model
_What did you struggle with?_
- None 
_What would you like to work on this week?_
- Ammend my model
- Start writing my thesis
- meet my supervisors
_Where do you need help with?
- N/A

**Rodney Omukuti**

_What did you achieve last week?_
- Worked on pangenomics
_Who did you help last week?_
- None
_Who helped you last week?_
- N/A
_What did you struggle with?_
- Building the pangenome graph
_What would you like to work on this week?_
- Explore on tools available for viruses
_Where do you need help?_
- Pangenomic tools specific for viruses

**Alex**

_What did you achieve last week?_
- MSA
_Who did you help last week?_
- None
_Who helped you last week?_
- N/A
_What did you struggle with?_
- None
_What would you like to work on this week?_
- data organization
- analysis
_Where do you need help?_
- None 
- 
## Hello & check in
## 30th May 2022
1. ken Murithi
2. Gladys Rotich
3. Rodney Omukuti



**Ken Mugambi**

_What did you achieve last week?_
- Data analysis 
_Who did you help last week?_
- None
_Who helped you last week?_
- N/A
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis objective 1 and 2
_Where do you need help?_
- N/A

**Gladys Rotich**
_What did you achieve last week?_
- Worked on objective 2
- Estimating R0
- Writing report on what I have gotten so far
- met my supervisors
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None 
_What would you like to work on this week?_
- Estimation of R0
- Document the transmission risk in Shimba Hills
- Start writing my thesis
- meet my supervisors
_Where do you need help?_
- N/A

**Rodney Omukuti**

_What did you achieve last week?_
- Worked on pangenomics
_Who did you help last week?_
- None
_Who helped you last week?_
- N/A
_What did you struggle with?_
- Building the pangenome graph
_What would you like to work on this week?_
- Explore on tools available for viruses
_Where do you need help?_
- Pangenomic tools specific for viruses

## Hello & check in
## 23rd May 2022
1. Caleb Kibet
2. Ken Murithi



## Hello & check in
## 16th May 2022
1. Ruth Nanjala
2. Denis Kinyugo
3. Maxwell Booker
4. Rodney Omukuti
5. Gladys Rotich
_Who did you help last week?_
- Interns
- John

_Who helped you last week?_
- Nehemiah

_What did you achieve last week?_
- Work with the interns
- John's work
- NGS training
- Imputation Manuscript
- Code review

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- NGS training
- Imputation Manuscript
- Interns code review and final presentation
- Discuss results with John

_Where do you need help?_
- N/A

**Gladys Rotich**
_What did you achieve last week?_
- Worked on objective 2
- Estimating R0
- Writing report on what I have gotten so far
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Meet my supervisors
- write report
- Start writing my thesis
_Where do you need help?_
- N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- NA

_What did you achieve last week?_
- Worked on the mini-project 

_What did you struggle with?_
- Creating and analyzing the pangenome 

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- Creating and analyzing the pangenome 

**Maxwell Booker**

_Who did you help this week?_
- Audrey

_Who helped you this week?_
- Ruth

_What did you achieve last week?_
- We worked on the analysis of the variants 
- Attended a Protein-Protein Docking Workshop 

_What did you struggle with?_
- N/A


_What would you like to work on this week?_
- Analysis of our Mini-project and Report

_Where do you need help?_
- N/A

**Rodney Omukuti**

_Who did you help last week?_
- NA

_Who helped you last week?_
- Worked with team members

_What did you achieve last week?_
- Worked on the mini-project 

_What did you struggle with?_
- Creating and analyzing the pangenome 

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- Creating and analyzing the pangenome 


## Hello & check in
## 9th May 2022
1. Ruth Nanjala
2. Ken Mugambi
3. Nyasita Ondari
4. Gladys Rotich
5. Denis Kinyugo
6. Rodney Omukuti
7. Sharon Watiri
8. Audrey Oronda
9. Maxwell Booker

_Who did you help last week?_
- Interns

_Who helped you last week?_
- N/A

_What did you achieve last week?_
- Work with the interns
- John's work

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- NGS training
- Imputation Manuscript
- Work with the interns
- Code review

_Where do you need help?_
- N/A


**Ken Mugambi**

_What did you achieve last week?_
- Data analysis 
_Who did you help last week?_
- None
_Who helped you last week?_
- N/A
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis objective 2
_Where do you need help?_
- N/A

**Nyasita Ondari**

_What did you achieve last week?_
- Data analysis 
_Who did you help last week?_
- None
_Who helped you last week?_
- N/A
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis objective 2
_Where do you need help?_
- N/A

**Gladys Rotich**
_What did you achieve last week?_
- Worked on objective 2
- Estimating R0
- Writing report on what I have gotten so far
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- Learning on using the Epimodel package in R
_What would you like to work on this week?_
- Estimation of R0
- Document the transmission risk in Shimba Hills
- Start writing my thesis
_Where do you need help?_
- N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- NA

_What did you achieve last week?_
- Worked on the mini-project 
- Attended PyCon

_What did you struggle with?_
- NA

_What would you like to work on this week?_
- Work on the mini-project 
- Present in Journal Club

_Where do you need help?_
- NA

**Rodney Omukuti**

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

_Who helped you last week?_
- Ruth

_What did you achieve last week?_
- Worked on the mini-project 

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- N/A

**Sharon Watiri**

_What did you achieve last week?_
* Mini-project

_Who did you help last week?_
* N/A

_Who helped you last week?_
* Ruth
* My team-mates

_What did you struggle with?_
* N/A

_What would you like to work on this week?_
* Mini-project

_Where do you need help?_
* N/A


**Audrey Oronda**

*Who did you help last week?*
- N/A

*Who helped you last week?*
-  Ruth

*What did you achieve last week?*

- Worked on the mini-project
- Making a report for the project

*What did you struggle with?*
- N/A

*What would you like to work on this week?*
- Work on the mini-project

*Where do you need help?*
- N/A

**Maxwell Booker**

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

_Who helped you this week?_
- Ruth

_What did you achieve last week?_
- We worked on the analysis of the variants we annotated

_What did you struggle with?_
- N/A


_What would you like to work on this week?_
- Analysis of the annotated variants
- Attending a Protein-Protein Docking workshop

_Where do you need help?_
- N/A

## Hello & check in
## 4th May 2022
1. Ruth Nanjala
2. Nyasita Ondari
3. Ken Mugambi
4. Sharon Watiri
5. Maxwell Booker
6. Denis Kinyugo
7. Rodney Omukuti
8. Gladys Rotich
9. Audrey OronOrondaOron


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

_Who helped you last week?_
- Dr.Caleb

_What did you achieve last week?_
- NGS Training
- Code review
- Work with the interns
- Imputation work
- Internship Manuscript
- John's work
- HLA typing work
- BHKi conference

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- NGS training
- Imputation Manuscript
- Assist John
- Work with the interns

_Where do you need help?_
- None

**Nyasita Ondari**
_Where do you need help?_
- None

_What did you achieve last week?_
- Corrections on 1st report
- Data analysis objective 2 & 3

_Who did you help last week?_
- None

_Who helped you last week?_
- None

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Corrections on first report
- Data analysis objective 2&3

_Where do you need help?_
- None

**Sharon Watiri**

What did you achieve last week?_
* Mini-project
* Attended the Bioinformatics and Open Science Skills Conference 

_Who did you help last week?_
* N/A

_Who helped you last week?_
* Dr.Caleb
* Ruth
* My team mates

_What did you struggle with?_
* N/A

_What would you like to work on this week?_
* Mini-project

_Where do you need help?_
* N/A


**Maxwell Booker**

_Who did you help this week?_
- N/a
_Who helped you this week?_
- Audrey, Ruth
_What did you achieve last week?_
- Working on our Miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject(Variant Annotation)
_Where do you need help?_
- N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- Dr Caleb
- Ruth

_What did you achieve last week?_
- Worked on the mini-project 

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- NA

**Rodney Omukuti**

What did you achieve last week?_
* Mini-project
* Bioinformatics and Open Science Skills Conference 

_Who did you help last week?_
* N/A

_Who helped you last week?_
* Dr.Caleb
* Ruth
* My team mates

_What did you struggle with?_
* N/A

_What would you like to work on this week?_
* Mini-project (pangenomics)

_Where do you need help?_
* N/A

**Gladys Rotich**
_What did you achieve last week?_
- Attended advanced bioinformatics course
- Estimating R0
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Estimation of R0
- Document the transmission risk in Shimba Hills
- Start writing my thesis
_Where do you need help?_
- N/A


**Audrey Oronda**

_Who did you help this week?_
- Maxwell
_Who helped you this week?_
- Maxwell, Ruth
_What did you achieve last week?_
- Working on our Miniproject
- Attended the Open Science and Bioinformatics Conference 
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject(Variant Annotation)
_Where do you need help?_
- N/A

## Hello & check in
## 25th April 2022
1. Ken Mugambi
2. Ruth Nanjala
3. Nyasita Ondari
4. Rodney Omukuti
5. Denis Kinyugo
6. Maxwell Booker
7. Gladys Rotich 
8. Audrey Oronda

**Ken Mugambi**
_What did you achieve last week?_
- Data analysis objective 2
- Attended advanced bioinformatics course
_Who did you help last week?_
- None
_Who helped you last week?_
- Ruth, Nehemiah
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis objective 2
_Where do you need help?_
- N/A


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

_Who helped you last week?_
- N/A

_What did you achieve last week?_
- NGS Training
- Code review
- Work with the interns
- Imputation work
- HLA typing work
- Internship Manuscript
- John's work

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- NGS training
- Imputation and Internship Manuscript
- Assist John
- Work with the interns
- HLA typing work

_Where do you need help?_
- None

**Nyasita Ondari**
_What did you achieve last week?_
- Attended advanced bioinformatics course
- Completed the first draft of objective 1 report
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis objective 2 & 3
_Where do you need help?_
- N/A

**Rodney Omukuti**
_Who did you help last week?_
- N/A

_Who helped you last week?_
- Andrew, Ruth, Kinyugo

_What did you achieve last week?_
- Code review
- Mini-project (pangenome)

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Mini-project (interpreting the pangenome)

_Where do you need help?_
- N/A

**Maxwell Booker**

_Who did you help this week?_
- N/a
_Who helped you this week?_
- Audrey, Ruth
_What did you achieve last week?_
- Got data for our Miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject(Variant calling)
_Where do you need help?_
- N/A

**Gladys Rotich**
_What did you achieve last week?_
- Attended advanced bioinformatics course
- Estimating R0
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Estimation of R0
- Attend advanced bioinformatics course
_Where do you need help?_
- N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- Ruth

_What did you achieve last week?_
- Worked on the mini-project 

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- NA

**Audrey Oronda**

_Who did you help last week?_
- Maxwell
_Who helped you last week?_
- Maxwell, Ruth
_What did you achieve last week?_
- Got data for our Miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject(Variant calling)
_Where do you need help?_
- N/A

## Hello & check in
## 19th April 2022
1. Gladys Rotich
2. Ruth Nanjala
3. Nyasita Ondari
4. Maxwell Booker
5. Nehemiah Ongeso
6. Sharon Watiri
7. Rodney Omukuti
8. Denis Kinyugo
9. Audrey Oronda

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

_Who helped you last week?_
- Dr. Caleb
- Pauline

_What did you achieve last week?_
- NGS Training
- Code review
- Work with the interns
- Imputation work

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- NGS training
- Imputation and Internship Manuscript
- Assist John
- Work with the interns
- HLA typing work

_Where do you need help?_
- None


**Gladys Rotich**
_What did you achieve last week?_
- Model analysis
- Attended advanced bioinformatics course
- Estimating R0
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Model validation 
- Estimation of R0
- Attend advanced bioinformatics course
_Where do you need help?_
- N/A

**Nyasita Ondari**
_What did you achieve last week?_
- Data analysis objective 2&3
- Attended advanced bioinformatics course
- Report drafting objective 1
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis objective 2
- Report drafting objective 1
- Attend advanced bioinformatics course
_Where do you need help?_
- N/A

**Maxwell Booker**

_Who did you help this week?_
- N/a
_Who helped you this week?_
- Audrey
_What did you achieve last week?_
- Starting our Miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
_Where do you need help?_
- N/A


**Sharon Watiri**

_What did you achieve last week?_
* Mini project
* jc presentation
_Who did you help last week?_
* N/A
_Who helped you last week?_
* My team mates
_What did you struggle with?_
* N/A
_What would you like to work on this week?_
* Mini project
_Where do you need help?_
* N/A

**Rodney Omukuti**

_What did you achieve last week?_
* Mini project
_Who did you help last week?_
* N/A
_Who helped you last week?_
* My team members
_What did you struggle with?_
* N/A
_What would you like to work on this week?_
* Mini project
_Where do you need help?_
* N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- Andrew
- Ruth

_What did you achieve last week?_
- Worked on the mini-project 

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- NA


**Audrey Oronda**

_Who did you help last week?_
- Maxwell
_Who helped you last week?_
- Maxwell
_What did you achieve last week?_
- Starting our Miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
- Seminar Presentation
_Where do you need help?_
- N/A

## Hello & check in
## 11th April 2022
1. Ruth Nanjala
2. Ken Mugambi
3. Gladys Rotich
4. Nyasita Ondari
5. Alex Gashanja
6. Maxwell Booker
7. Nehemiah Ongeso
8. Audrey Oronda
9. Sharon Watiri
10. Rodney Omukuti

**Ken Mugambi**

_Who did you help last week?_
- None

_Who helped you last week?_
- My supervisors
- My fellow MSc students

_What did you achieve last week?_
- Objective 2 - information content
- Progress presentation (Pwani University)
- Progress presentation (Monday Morning)

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Data analysis for objective 2 
- Manual gene curation
- Lay plans for the third objective

_Where do you need help?_
- None

**Gladys Rotich**
_What did you achieve last week?_
- Met supervisors
- Project progress presentation- Pwani University
- Model analysis
- Attended advanced bioinformatics course

_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Model validation and analysis
- Estimation of R0
- Attend advanced bioinformatics course
_Where do you need help?_
- N/A


**Nyasita Ondari**
_What did you achieve last week?_
- Met supervisors
- Project progress presentation
- Attended advanced bioinformatics course

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

_Who helped you last week?_
- N/A

_What did you struggle with?_
- N/A

_What would you like to work on this week?_
- Report writing - objective 1
- Docking - objective 3

_Where do you need help?_
- N/A

**Alex Gashanja**

_Who did you help last week?_
- Ken, Laurah, Gladys

_Who helped you last week?_
- Ken, Laurah, Gladys

_What did you achieve last week?_
- Received feedback for my progress report ppt slides
- presented my progress at the university
- Filtered my dataset

_What did you struggle with?_
- None

_What would you like to work on this week?_
- QC, Genome assembly, annotation, Variant calling
- Attend advanced bioinformatics course

_Where do you need help?_
- N/A

**Maxwell Booker**

_Who did you help this week?_
- Audrey
_Who helped you this week?_
- Ruth, Audrey
_What did you achieve last week?_
- LAB tours by Dr.Villinger
- Starting our Miniproject
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
_Where do you need help?_
- N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- Dr Caleb
- Pauline 

_What did you achieve last week?_
- Presented final results on phylogenetics mini-project 
- Worked on the mini-project 


_What did you struggle with?_
- None

_What would you like to work on this week?_
- Work on the mini-project 

_Where do you need help?_
- NA

**Audrey Oronda**

_Who did you help this week?_
- Maxwell
_Who helped you this week?_
- Ruth, Maxwell, Pauline
_What did you achieve last week?_
- LAB tours 
- Starting the Miniproject
- Finalized on the reproducibility paper
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- Test run on the miniproject
_Where do you need help?_
- N/A

**Sharon Watiri**

What did you achieve last week?
* MBBU, EID lab tour
* Worked on the mini project 
* First code review

Who did you help last week?
* N/A

Who helped you last week?
* Ruth, 
* Dr Caleb,
* my team mates

What did you struggle with?
* N/A

What would you like to work on this week?
* Mini project
* Journal Club presentation

Where do you need help?
* N/A

**Rodney Omukuti**

What did you achieve last week?
* MBBU, EID lab tour
* Worked on the mini project 
* First code review

Who did you help last week?
* N/A

Who helped you last week?
* Ruth, 
* Dr Caleb,
* my team mates

What did you struggle with?
* N/A

What would you like to work on this week?
* Mini project

Where do you need help?
* N/A

**Ruth Nanjala**

_Who did you help last week?_
- Interns

_Who helped you last week?_
- Dr. Caleb
- Pauline

_What did you achieve last week?_
- NGS Training
- BWCB JC
- Carpentries workshop
- MBBU tour
- Code review
- Work with the interns

_What did you struggle with?_
- Laptop hardware

_What would you like to work on this week?_
- NGS training
- Manuscript
- Assist John
- Work with the interns

_Where do you need help?_
- None


## Hello & check in
## 4th April 2022
1. Ruth Nanjala
2. Gladys Rotich
3. Nyasita Ondari
4. Alex Gashanja
5. Ken Mugambi
6. Caleb Kibet
7. Sharon Watiri
8. Maxwell Booker
9. Rodney Omukuti
10. Denis Kinyugo
11. Audrey Oronda


**Ruth Nanjala**
_Who did you help this week?_
- Interns
- John
_Who helped you this week?_
- Laura, Dr.Caleb
_What did you achieve last week?_
- BOSS conference planning
- Introducing the Interns miniprojects
- Training Aga Khan students
- H3ABioNet & Wellcome Connecting Science NGS training
- International Symposium on human genetics
- John's project
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Imputation manuscript
- Coordinating internship activities (lab tour)
- National Institute for theoretical Sciences Carpentries workshop
- John's project
- BWCB Journal Club
_Where do you need help?_
- None

**Gladys Rotich**

_Who did you help last week?_
- None
_Who helped you last week?_
- Dr. Caleb
_What did you achieve last week?_
- Model plotting
- model analysis
- Prepare for school presentation
_What did you struggle with?_
- Estimating model parameters
_What would you like to work on this week?_
- Model analysis
- school presentation
- estimation of the basic reproduction number
- meet my supervisors
_Where do you need help?_
- N/A


**Nyasita Ondari**

_Who did you help last week?_
- None

_Who helped you last week?_
- My supervisors

_What did you achieve last week?_
- Finished objective 1
- Identified potential targets for the new drug
- University of Cambridge SARS cov genome analysis course

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Data analysis for objective 2&3
- Masters project presentation
_Where do you need help?_
- None


**Alex Gashanja**
_Who did you help last week?_
- None
_Who helped you last week?_
- Dr. Caleb
_What did you achieve last week?_
- Writing a progress report
_What did you struggle with?_
- None
_What would you like to work on this week?_
- progress report presentation
_Where do you need help?_
- None


**Ken Mugambi**

_Who did you help last week?_
- None

_Who helped you last week?_
- My supervisors

_What did you achieve last week?_
- Objective 2 - motif comparison
- Powerpoint 

_What did you struggle with?_
- Motif comparison

_What would you like to work on this week?_
- Power point presentation (Pwani university)
- Data analysis for objective 2

_Where do you need help?_
- None




**Caleb Kibet**
_What did you achieve last week?_
- Writing (manuscript, grants)
- Meetings and Supervision
- Interns mini-projects
- RSE, H3ABionet working group
- Admin stufff

_Who did you help last week?_
- Alex, Ken
_Who helped you last week?_
- Laura and Ruth
_What did you struggle with?_

_What would you like to work on this week?_
- Student work review (Manuscripts, proposals, presentations, Thesis)
_Where do you need help?_
- NGS training

**Sharon Watiri**

_What did you achieve last week?_

* CV and  cover letter writting training
* Introduction to the mini projects

_Who did you help last week?_
*  N/A

_Who helped you last week?_
* Ruth, Dr. Caleb

_What did you struggle with?_
* N/A

_What would you like to work on this week?_
* Mini projects
* lab tour

_Where do you need help?_
* N/A


**Maxwell Booker**

_Who did you help this week?_
- Audrey
_Who helped you this week?_
- Ruth, Dr. Caleb
_What did you achieve last week?_
- JC presentation 
- Training on CV and Resume writing
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
- lab tours
_Where do you need help?_
- N/A

**Rodney Omukuti**

_Who did you help this week?_
- N/A
_Who helped you this week?_
- Ruth, Dr. Caleb
_What did you achieve last week?_
- Introduction to the mini-project
- Training on CV and Resume writing
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- mini-project
- lab tour
_Where do you need help?_
- N/A

**Denis Kinyugo**

_Who did you help last week?_
- NA

_Who helped you last week?_
- NA

_What did you achieve last week?_
- Attended a workshop on resume and cover letter writing
- Annotated the phylogenetic tree for the mini-project
- Formulated a work schedule on how to tacke the mini-project

_What did you struggle with?_
- None

_What would you like to work on this week?_
- Draw insights from the phylogenetic tree 
- Work on the mini-project 

_Where do you need help?_
- NA

**Audrey Oronda**

_Who did you help this week?_
- N/A
_Who helped you this week?_
- Ruth, Dr. Caleb, Maxwell
_What did you achieve last week?_
- Annotating the phylogenetic tree from the paper we were reproducing 
- Training on CV and Resume writing
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
- lab tours
_Where do you need help?_
- N/A

## Hello & check in
## 28th March 2022
1. Ruth Nanjala
2. Gladys Rotich
3. Nyasita Ondari
4. Ken Mugambi
5. Sharon Watiri
6. Maxwell Booker
7. Rodney Omukuti
8. Audrey Oronda

**Rodney Omukuti**

_Who did you help this week?_
- N/A
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Attended an Information literacy workshop, 
- African Bee Health lab tour
- library tour
- Miniproject final presentation
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
_Where do you need help?_
- N/A

What did you achieve last week?

*Final presentations on the mini projects*
 *Attended the information literacy workshop*
 *Library and Bee health lab tour*

Who did you help last week?

*N/A*

Who helped you last week?

*Ruth, Pauline*

What did you struggle with?
*N/A*


What would you like to work on this week?
*Introduction  to the mini project*

Where do you need help?
*N/A*

**Ruth Nanjala**

_Who did you help this week?_
- Interns
_Who helped you this week?_
- Laura, Ken, Pauline, ALex, Dr.Caleb
_What did you achieve last week?_
- Coordinating internship activities (workshop, lab tour, library tour)
- Internship manuscript
- Interns final miniproject presentation
- H3ABioNet & Wellcome Connecting Science NGS training
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Imputation manuscript
- BOSS conference planning
- Introducing the Interns miniprojects
- NGS workshop 
_Where do you need help?_
- None

**Gladys Rotich**
_What did you achieve last week?_
- Review vector model
- Start plotting the Host model
_Who did you help last week?_
- None
_Who helped you last week?_
- None
_What did you struggle with?_
- Estimating host model parameters
_What would you like to work on this week?_
- Finish on host model
- meet my supervisors
- prepare for project progress presentation
_Where do you need help?_
- None


**Nyasita Ondari**
_Who did you help this week?_
- N/A
_Who helped you this week?_
- Maxwell
_What did you achieve last week?_
- Data analysis
- Meeting with supervisors
_What did you struggle with?_
- None
_What would you like to work on this week?_
- Data analysis
_Where do you need help?_
- None

**Ken Mugambi**
_Who did you help this week?_
- Ruth
_Who helped you this week?_
- Dr.Caleb, Pauline 
_What did you achieve last week?_
- Data analysis
- Meeting with supervisors
_What did you struggle with?_
- Data interpretation
_What would you like to work on this week?_
- Data analysis
_Where do you need help?_
- None

**Denis Kinyugo**
_Who did you help this week?_
- NA
_Who helped you this week?_
- Ruth, Pauline, Andrew 
_What did you achieve last week?_
- Running the full pipeline for mini-project 
- Read more on phylogenetics
_What did you struggle with?_
- NA
_What would you like to work on this week?_
- Finish analysing our mini-project phylogenetic tree 
_Where do you need help?_
- NA

**Maxwell Booker**

_Who did you help this week?_
- Laurah
_Who helped you this week?_
- N/A
_What did you achieve last week?_
- Attended an Information literacy workshop, 
- African Bee Health lab tour
- library tour
- Miniproject final presentation
_What did you struggle with?_
- N/A
_What would you like to work on this week?_
- miniproject
- Journal Club Paper
_Where do you need help?_
- N/A

**Audrey Oronda**
_Who did you help this week?_
- NA
_Who helped you this week?_
- Ruth, Pauline, Kinyugo 
_What did you achieve last week?_
- Running the full pipeline for mini-project 
- Read more on phylogenetics
_What did you struggle with?_
- NA
_What would you like to work on this week?_
- Finish analysing our mini-project phylogenetic tree 
_Where do you need help?_
- NA