# Cohort 6 intern mini-projects

## Project 1: Working with the cloud and HPC
Assign: Cynthia

The Molecular Biology and Bioinformatics Unit (MBBU) provides relevant expertise to facilitate molecular biology and bioinformatics components of *icipe* research across themes while spearheading research projects that employ and develop cutting-edge molecular and bioinformatics techniques applicable to modern insect science. The Bioinformatics strategy centred on building human infrastructure and analysis capacity to support genomics research at *icipe*. One of the Key components of this is for the user to provide sufficient computing resources for the centre through the HPC, the AWS cloud and the Desktop computers.

The purpose of this Project is to review the current state of our infrastructure, starting with the desktop computers, the HPC, and ultimately the cloud.
In the Project, you will be required to:
1. Establish an HPC system that uses three desktop computers running on CentOS, complete with job management, job monitoring, and user management and storage monitoring alerts.
1. Understand and document the current HPC architecture
2. Provide recommendations (from research and testing) on how we can optimize the system (especially storage management)
3. Solutions for data management within the system
4. Review and provide recommendations for moving some of the HPC loads to the cloud. How can the system be secured, how should the accounts be managed, and how can we optimize costs?

## Project 2: Tick Metagenomics
Assign:
- Mark
- Jimmy
- Ann

**Mark**
Metagenomics is the sequencing of all the genetic materials available in the sample. Identifying the microorganisms available in the sample depends on a database match compounded by the exhaustiveness of the databases, the ubiquity of some microbes, the sequencing depth and the analysis approach. This study explores how alternative means of analyzing tick metagenomic data can affect the results. The study will use the paper data provided in [this paper](https://www.frontiersin.org/articles/10.3389/fmicb.2022.932224/full) to reproduce it, analyze using alternative techniques, and explore what that would mean for the results.

**Ann**
**Additional Tasks**: Visualization of the 16s results output from a Bee metagenomics analysis already done.

## Project 3: Metabarcoding of Rumen Microbiome

Assign:
- Vanesa
- Samwel
- Victor

**Victor**
This Project aims to **establish rumen microbiome diversity and variation between cattle, camels, goats and sheep**. Genomic rumen microbiome DNA was isolated and characterized using bacterial and archaeal 16S rRNA, protozoal 18S rRNA genes and fungal ITS1 gene amplicons sequencing from the harvested bovine rumen fluid samples using next-generation sequencing technology.

For this Project, you are provided with 160 fastq samples generated using multiple primers. In addition to establishing the diversity, especially for the 16S data, you are expected to perform functional analysis.
Resources: https://github.com/mbbu/Reviewing-16s-Analysis-Workflows