Kevin Rue-Albrecht (Ph.D, Dipl. Ing.)

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# Kevin Rue-Albrecht (Ph.D, Dipl. Ing.) <img src="img/sticker.png" alt="logo" height="120px" style="float:right">
## SSI Fellowship 2021 - Application
### <a href="https://kevinrue.github.io"> kevinrue</a> <a href="https://twitter.com/KevinRUE67"> KevinRUE67</a> <a href="https://www.linkedin.com/in/kevin-rue-albrecht/"> kevin-rue-albrecht</a>
### 2021-02-05 (updated: 2021-01-27)

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Kevin Rue-Albrecht
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;
SSI Fellowship Application 2021
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# About me

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Computational Biologist
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# 2021 Fellowship Program

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# More about me

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Using *[leaflet](https://CRAN.R-project.org/package=leaflet)*
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# A bird's-eye view of my programming journey

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```
>> fprintf 'Hello, Matlab!'
```

```
>>> print("Hello, Python!")
```

```
> cat("Hello, R!")
```

```
<script>
 alert( 'Hello, JavaScript!' );
</script>
```

]

.pull-right[
```
SELECT COUNT(*) FROM hellosql;
```

```
echo "Hello, Unix!"
```

```
<html>
 <body>
 Hello, HTML!
 </body>
</html>
```
]

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# GOexpress

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<img src="img/logo-bioconductor.png" height="200px" alt="Bioconductor hexsticker"></img>

<img src="img/logo-goexpress.png" height="200px" alt="GOexpress hexsticker"></img>

<https://bioconductor.org/packages/GOexpress>
]

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# Ph.D. Research

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<img src="img/article-tuberculosis.png" height="450px" alt="Bioconductor hexsticker"></img>
]

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<https://doi.org/10.3389/fimmu.2014.00536>
]

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# Continuing contributions to the Bioconductor project

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<https://bioconductor.org>

<https://bioconductor.org/packages/TVTB> (2016)

<https://bioconductor.org/packages/iSEE> (2018)

<https://bioconductor.org/packages/iSEEu> (2020)
]

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# iSEE - Interactive SummarizedExperiment Explorer

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<img src="img/isee-interface.png" height="500px" width="600px" alt="iSEE user interface"></img>
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# Most technically impressive app

.center[
<img src="img/logo-isee.png" height="300px" align="middle" alt="iSEE hexsticker"></img>

<img src="img/isee-shiny-contest.png" height="400px" align="middle" alt="Shiny contest logo"></img>
]

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<https://blog.rstudio.com/2019/04/05/first-shiny-contest-winners>
]

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# GitHub organisation

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<img src="img/github-isee-organisation.png" height="450px" alt="iSEE organisation on GitHub"></img>
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<https://github.com/iSEE>
]

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# OBDS Training Programme

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<img src="img/ox_brand1_pos_rect.gif" alt="University of Oxford logo"></img>
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## Instructor

- Unix and HPC environments

- Conda

- Git and GitHub

- Python

- R and Bioconductor
]

.pull-right[

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[www.imm.ox.ac.uk](https://www.imm.ox.ac.uk/research/units-and-centres/mrc-wimm-centre-for-computational-biology/training/oxford-biomedical-data-science-training-programme)
]
]

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# Co-organiser & Contributor

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<img src="img/bioc2021-page.png" alt="Bioconductor conference 2021"></img>
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<img src="img/logo-thecarpentries.svg" alt="The Carpentries logo"></img>
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# My fellowship plan

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# 1. Local & Online events

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- Thematic workshops

- Software Carpentry

- DevOps (CI/CD, unit testing, GitHub Actions, containerisation)

- Blog posts and videos

+ <https://kevinrue.github.io>
 
 + [iSEE playlist](https://www.youtube.com/playlist?list=PLOsChEX1ArWEwkPUTeQK9fhNB96LQJm5H)
]

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# 2. Expanding the iSEE universe

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- New panels to support more data types

+ e.g., <https://github.com/jgilis/iSEEtranscripts>

- Online workshops

+ e.g. <https://isee.github.io/iSEEWorkshopEuroBioc2020>

- iSEE book

+ <https://isee.github.io/iSEE-book>

- Deployment, accessibility, scalability
]

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# 3. Collaboration

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- BiocChallenges <img src="img/logo-biocchallenges.png" alt="BiocChallenges logo" height="200px" align="right"></img>

+ <https://kevinrue.github.io/BiocChallenges>

- BiocSpatialChallenges

+ <https://helenalc.github.io/BiocSpatialChallenges>
]

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# Fellowship: 3 goals

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Local & Online Educational Events

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Expand the iSEE universe

&emsp;
Collaborate on open-source challenges
]

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# Software Sustainability Institute

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<img src="img/ssi-manifesto.png" height="500px" alt="SSI manifesto"></img>

]

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# We are all standing on the shoulders of giants

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<img src="img/hexsticker-wall.jpg" height="500px" alt="useR hexsticker wall"></img>

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