# Competence table UPPMAX

**Regarding tickets**

[TOC]

## Background

### Problem
- We all have other duties other than ticket solving
- We don't have the time to solve them all in relevant time
- "Sourdoughs" that are not touched for months
- Some competences are owned by just 1-2 people
- One takes the ticket and thinks that I'll do it soon
- time flies and "let's take this new interesting ticket (and forget(?) the old ones?)"
- Pavlin and Björn often go through tickets and look for an AE that can take it
- but sometimes no answer
- Licenses
- please add info in [HackMD page](https://hackmd.io/MWPiyLaERKyXRvpUP2WOew)

### Needs
- reduce the number of topics with just one expert
- bioinformaticians are needed for some "runtime tickets", not always easy to reach out to you
- what are the sub-areas in bio that you are good at (Björn's not sure)
- get to know how much we can count on you
- how many percent available for support questions

### Some status

- [Application experts page needs update](https://www.uu.se/en/centre/uppmax/about-us/application-experts)
- is lacking many new employees
- explains more the background of some personnel
- but not the ticket expertises
- In [UU catalogue](https://www.uu.se/en/centre/uppmax/contact)
- listed as AE or bioinformatician
- perhaps not valid?
### Way forward?

- Let us find the ticket-related competences?
- I know SUPR has it but is not as of today shared
- language
- tools
- architecture
- "biothinking" and research-specific workflow
- Identify some topics were more people can be involved
- existing competence not used?
- competence development
- examples
- containers
- nextflow
- CUDA/GPU
- Easybuild
- licenses
- biodatabases

## Questions

- Can we distribute bioinfo database questions from users
- **reason**: they tend to take more time to answer. Doug is often alone on these
- Pavlin and me often ask for input from a bioinformatician.
- rather often we get no response
- can we pin all of you @bioinformaticians?
- and expect an answer
- what are your specific competences therein

## ToDos

- **Please fill out the [matrix](https://hackmd.io/BLnKr2C-Rl6myqDlb9BP4w?both#Matrix-of-problematic-competences) and [details lists](https://hackmd.io/BLnKr2C-Rl6myqDlb9BP4w?both#Application-expert-personnel-and-percent-available) below**
- feel free to add stuff

## Matrix of problematic competences

- Abbreviated names, see [list below](https://hackmd.io/BLnKr2C-Rl6myqDlb9BP4w?both#AEs-general)

- Scale
1. To some degree
2. Pretty used with

### General

Competence |RB|BC|DI|PM|DS|JY|ML|JS|LE|
-|-|-|-|-|-|-|-|-|-|
CUDA |0 |0 |2 |0|1?|1||0|1
C++ |2 |1 |2 |?|?|1|?|1|2
EasyBuild |0 |1 |2 |1|2|0||0|-
Matlab |0 |2 | |0||1|1|1|
Julia |0 |1-2| |1||0||0|1
Nextflow |1 |0 |0+|2|?|0|?|0
Python |2 |2 |2 |2|?|2|?|1|2
R |2 |1 | |-1|?|0|1|1
Rust |2 |0 | |0|?|0|?|0|0
Singularity|2 |0+ | |2|?|1|?|?|
please add!||||||||

### Bioinfo/LifeScience
- Databases are of course many and can occupy several lines below
- installing and linking
- help users also choose or get understanding
- Research workflows (not necessarily pipelines)
- Knowing tools and their parallelism possibilities

Competence|RB|DS|JS|MD|BV|LE|PM|JS
-|-|-|-|-|-|-|-|-
nextflow|1||||||2|1
databases||x|||||0
-kraken (more to add)||x|||||
bio research workflows (specific topics below)||||||||
-Immunology|2|||||||
-RNA|1|||||||1
-phylogenetics|2|||||||1
please add!|||||||

## Application expert personnel and percent available

- where are our competences?
- comp languages
- specific tools/software
- architecture
- "biothinking" and research-specific workflow
- is something lacking?
- I want to learn more about... so that we fill gap or relieve that work of others
- Example: Björn should learn
- create containers
- more about julia
- eb files

### AEs (general)
- Percentage means time available for tickets

- **RB** Richel Bilderbeek: AE 100%
- Anything biology, specialized in phylogenetics and immunology
- C++
- Nextflow
- Python
- R
- Rust
- Singularity
- I want to learn more about...
- Allocations
- Anything biology
- Software installation

- **BC** Björn Claremar: AE 30%
- matlab
- python/conda
- julia
- R packages (RStudio)
- (fortran)
- installations
- specific tools/software
- WRF
- general superficial understanding of other
- want to learn more about
- building containers
- julia
- eb files

- **LE** Lars Eklund: AE (and/or Bioinformatician)
- **DI** Diana Iusan: AE
- EasyBuild and "manual" installs
- Materials Theory codes: VASP, ORCA, Amber, RSPt, ...
- **ML** Marcus Lundberg: AE / coordinator
- **PM** Pavlin Mitev: AE
- Installations
- Nextflow
- Singularity
- Cloud - as user
- Codes in computational chemistry/physics: VASP, CASTEP, cp2k, Molecular and Lattice Dynamics in general
- Other codes: Octave, Awk, Python, Fortran
- Other tools: spack, pixi
- **DS** Douglas Scofield: AE (much bioinfo but not bioinformatician?)
- **BV** Björn Viklund: AE (and/or Bioinformatician)
- **JY** Jayant Yadav: AE/Humaniora+ML 50%
- Python
- Installations
- Cloud and containerization
- ML models and GPU
- Visualizations
- Want to learn: CUDA

### Bioinformaticians
- **MD** Martin Dahlö: Bioinformatician
- **JS** Jonas Söderberg: Bioinformatician
- **LE** *Lars Eklund: AE (and/or Bioinformatician)*
- **BV** *Björn Viklund: AE (and/or Bioinformatician)*
- **RB** *Richel Bilderbeek: AE (and/or Bioinformatician)*
- **DS** *Douglas Scofield: AE (much bioinfo but not bioinformatician?)*

### Allocations
- Anders Sjölander: AE/allocation
- Rebecca Söderberg: AE/allocation