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• 2018-02-01 | career

  Zürich Life Science Day 2018: presentation and impressions

  Zürich Life Science Day is a one-day event organised by the Life Science Zurich Young Scientist Network, mostly students from ETH and Univeristy of Zürich, that aims at introducing career opportunities to students and young professionals in life science. Beyond booths and stands by academic institutes and companies, career opportunities in both academics and industry are presented by speakers with years of first-hand experience in respective functions and positions.

• 2018-01-20 | programming

  Develop R packages with Rcpp and RStudio

  Recently, I updated the ribiosMath package. The aim was to increase the efficiency of several commonly used computational procedures (Kappa’s statistic, cosine similarity, etc.) by implementing them in C++.

• 2018-01-16 | programming

  Notes on using sqlite3

  Below we assume that the SQLite3 database is stored in a file ‘mydb’

  • To list all tables in a database

      sqlite3 mydb .tables
    

    In an interactive session, .tables can be also used to list all tables.

  • To print the schema of a database into a text file

      sqlite3 mydb .schema > mydb_schema.sql
    

  • To list the first 10 rows of a table (mytable) in an interactive session

      SELECT * FROM mytable WHERE ROWID<=10;
    

  • To use foreign keys in sqlite3, say column ParentID in table ChildTable should reference the column ID in table ParentTable

      CREATE TABLE ParentTable (
        ID INTEGER PRIMARY KEY,
        NAME TEXT
      );
      CREATE TABLE ChildTable (
        ID INTEGER PRIMARY KEY,
        ParentID INTEGER,
        NAME TEXT,
        FOREIGN KEY(ParentID) REFERENCES ParentTable(ID)
      );
    

    Notice that in the last parameter of create table, ParentID is used as a parameter of the function FOREIGN KEY, and the parent table and foreign key column are defined by the format ParentTable(ID). The two parentheses are interpreted differently.

• 2018-01-09 | 

  Pharmacogenomics of GPCR Drug Targets

  During the Christmas break I stumbled upon a very interesting paper published in Cell, Pharmacogenomics of GPCR Drug Targets (open access). I liked the paper, because it points a way forward to personalised pharmacology and safety.

• 2018-01-04 | machine-learning

  Ridge regression, LASSO, and elastic net explained

  glmnet is a R package for ridge regression, LASSO regression, and elastic net. The authors of the package, Trevor Hastie and Junyang Qian, have written a beautiful vignette accompanying the package to demonstrate how to use the package: here is the link to the version hosted on the homepage of T. Hastie (and an ealier version written in 2014).