IDS Coding Club

Julia vs Python

Fabian presented a summary of an article that he read recently about the programming language ‘Julia’. It was presented as a comparison with other programming languages that we might be more familiar with (mainly Python). Really nice to see how the new language tries to get the best features of other languages (speed of C, general usage from Python, great math/stats from R, etc.)

bioinformatics

Snelle methode voor vergelijken van isolaten binnen hetzelfde species

Today it was Amber’s last presentation before she leaves the RIVM. She has been working here for more than 10 years but she will now start a new challenge as a data scientist. She, however, gave a very nice presentation about the methods she has used to compare (fungal) isolates within the same species. She mainly talked about the Split Kmer Analysis (SKA) toolkit for SNP analysis. She also mentioned her experience with iq-Tree for making phylogenetic trees and with iTOL to visualize them.

R

Seurat - Single cell R toolkit

Roxanne presented the basics of using the Seurat package for doing single-cell RNA-seq analysis.

python

BioPandas

Varisha presented the release of BioPandas and the features it includes.

programming

Bash scripting

Alejandra talked to us about basic concepts of a shell and programming vs scripting. She also highlighted some of the good practices in coding using BASH and we look at some code examples.

juno

Logo Design for Juno pipelines

Roxanne has been designing some logos for the pipelines that we have developed to analyse bacteriology genomes. She took input from the mythology, from the work we do and from her knowledge in design. She presented her current designs and asked for our input to decide which logo will be used as the official one for the Juno pipeline. We almost unanimously decided on the ‘peacock inspiration’ and that is the one that will be used (with different text per pipeline)

programming

Coding in Space

Fabian merged his passion for space exploration and astronomy into our programming club and he presented some examples on how important programming is for NASA and for space missions.

python

Natural Language Processing project

Roxanne has been designing some logos for the pipelines that we have developed to analyse bacteriology genomes. She took input from the mythology, from the work we do and from her knowledge in design. She presented her current designs and asked for our input to decide which logo will be used as the official one for the Juno pipeline. We almost unanimously decided on the ‘peacock inspiration’ and that is the one that will be used (with different text per pipeline)

Bioinformatics pipelines with Snakemake

At the IDS we mainly use Snakemaketo make pipelines so we decided to go over the documentation. It was my turn (Ale) to present and since I am the most experience with Snakemake, I could dig into it and try to give proper working examples. fitvids('.shareagain', {players: 'iframe'});

Introduction to mGWAS

GWAS Genetische varianten associëren met een fenotypische eigenschap Supervised machine learning task INHOUD Humane/microbiële GWAS Tools Random Forest in R Scoary Scikit learn GWAS van Aspergillus Pyseer HUMANE GWAS Eerste studie gepubliceerd in 2002 1133 patiënten met een hartinfarct 2 controle groepen van in totaal 1878 personen 92,788 gene-based SNP markers Linkage disequilibrium mapping (association mapping)

Web Development - Roxanne

INTERACTION-DESIGN & DEVELOPMENT STUDY TIMELINE YEAR 1 YEAR 2 YEAR 3 YEAR 4 GRADUATIONAFTER - Media design - Web design - Web development - Game design - 3D - Focus on design - Fonts - Spacing - Color schemes - Front end development using HTML5 & CSS - Introduction JavaScript - Back-end development with PHP and WordPress - First internship - Second internship - Start content writing - Graduation project - Web design & development - Content writing - Edit pictures, logos, corporate designs etc.

about

Intro and house rules

The idea Once a week for 1 h. Concept: Share article (microbial genomics or related) or a library or something interesting you found that week. Ask a specific question. Explain one algorithm. Practice for a presentation in a conference. Discuss pipeline/software design. Some sessions reserved for CODE REVIEW (see principles and house rules). … No need of presentation or anything formal… unless you want it.