# Keenan Ikking

Keenan Ikking is a remote worker on Himalayas, Software Developer at BioInformatiCo, based in South Africa.

Source: https://himalayas.app/@keenanikking

```text
Software developer at BioInformatiCo building Java document pipelines and R clinical-reporting frameworks; improved usable trial protocols from 7 to 19.
```

| Detail | Value |
| --- | --- |
| Availability | Looking for a job |
| Location | South Africa |
| Authorized to work in | South Africa |
| Salary expectations | 40k+ ZAR |
| Job categories | Software Developer, Backend Engineer, Data Engineer |
| Skills | Java, R, Python, Data Pipelines, Software Architecture, Pipeline Orchestration, Test Driven Development, Domain Driven Design, LLM Pipeline Evaluation, Clinical Data Management, Clinical Reporting, Bioinformatics, Statistical Analysis, SQL, BASH |
| GitHub | https://github.com/Kikking |

## What I'm looking for

```text
I'm looking for a backend or data engineering role with hard problems in pipelines, design, and performance.
```

## About

```text
At BioInformatiCo, I built a multi-stage Java pipeline that turns raw PDF geometry into structured logical sections. I also redesigned file uploads so new types can be added through configuration rather than shared-code changes.

I built a testing environment to distinguish retrieval misses from LLM misreads, helping raise usable trial protocols from 7 to 19. I introduced reference outputs and used precision, sensitivity, and F1 scores to validate pipeline results.

I designed an R-based DataFlow framework for clinical-trial reporting and programmed Safety Summary and Safety History reports through UAT cycles. For a difficult clinical report, I used test-driven development and a single test row mutated across 21 assertions to support a fast build and absorb QC fixes without regressions.

At the University of the Witwatersrand's Gentle Lab, I built and published nano-pipe, an open-source long-read RNA analysis pipeline, and developed benchmarking and evaluation pipelines for isoform-discovery tools. I have an MSc in Applied Bioinformatics with distinction, and I'm looking for a backend or data engineering role tackling hard problems in pipelines, design, and performance.
```

## Experience

### Software Developer (current)

BioInformatiCo. Jan 2025 - Present

```text
Built multi-stage document understanding pipelines in Java and an R-based DataFlow framework for regulated clinical reports. Improved LLM pipeline evaluation, raising usable trial protocols from 7 to 19.
```

Skills: Java, R, Python, SQL, AWS, S3, Docker, Podman, Linux, Git, GitHub, Test-Driven-Development, Domain-Driven-Design, Pipeline-Orchestration, LLM-Pipeline-Evaluation

### Postgraduate Researcher

University of the Witwatersrand, Gentle Lab. Jan 2023 - Jan 2025

```text
Built and published nano-pipe, an open-source long-read RNA analysis pipeline, and developed fault-tolerant benchmarking pipelines for isoform discovery tool evaluation.
```

Skills: Python, R, BASH, Git, GitHub, Pipeline-Development, Benchmarking, RNAseq, Long-Read-Sequencing, Isoform-Discovery

### Teaching Assistant

University of the Witwatersrand. Jan 2022 - Jan 2024

```text
Taught third-year Bioinformatics Python practicals for two years.
```

Skills: Python, Teaching, Bioinformatics

## Education

### University of the Witwatersrand

Master of Science, Applied Bioinformatics. 2023 - 2025. Grade: With Distinction

```text
Master of Science in Applied Bioinformatics with distinction, specializing in performant pipelines for big data simulations and statistical methods for large datasets. Presented research at four conferences and symposiums.
```

### University of the Witwatersrand

Bachelor of Science Honours, Applied Bioinformatics. 2022 - 2022

```text
Bachelor of Science Honours in Applied Bioinformatics.
```

### University of the Witwatersrand

Bachelor of Science, Genetics, Bioinformatics and Microbiology. 2019 - 2021

```text
Bachelor of Science in Genetics, Bioinformatics and Microbiology.
```

## Tech stack

- GitHub
- IntelliJ IDEA
- React
- Svelte
- JavaScript
- Python
- Java
- Linux
- Git
- Docker
- SQL
- Podman
- Bash
- Conda

To contact Keenan, message them from this profile with a Himalayas employer account: [Hire on Himalayas](https://himalayas.app/hire).

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