Subscribe Posts by category By tags

Recent posts

• 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).

• 2016-11-18 | medchem

  edX Medicinal Chemistry - chapter one

  I follow course DavidsonX: D001x Medicinal Chemistry on edX. Here are the notes.

• 2016-11-12 | 

  Start of the blog

  I start the blog project to take notes of things I learn as a computational biologist working in drug discovery.