DBW - Databases and Web development. 20254-26 Individual Exercises (Deadline 15th March)

Personal web site

A free format and contents personal web site, installed at server. It should include:

• Links to Solved exercises (below)
• A "project" section including link to the presentations and link to the running application
• Note that the personal web site should be the default entry of your personal web site (use index.xxx)

Web application to execute an external program (CLUSTAL-Omega)

Prepare a web application (php or python/flask, running in the course server) to perform multiple sequence alignment using Clustal-Omega (executable can be obtained from https://www.clustal.org).
It should have

• Alternative Input options (Note that input format should be recognized by the application, do not use input selectors)
  • A set of protein sequences (in FASTA)
  • A set of Uniprot ids (sequences could be obtained from https://www.uniprot.org/uniprot/{id}.fasta)
  • A set of PDB Ids (sequences could be obtained from https://www.rcsb.org/fasta/entry/{id})
  • A File upload (FASTA format)
• Program options (minimum set):
  • output format
  • (Optional) other Clustal-O options
• check input for errors (e.g. Unkown format, No sequences available, ...) and give meningful messages
• format the output (be aware of the possible output formats), and allow to download results.

Recommended procedure:

1. Prepare a local installation of ClustalO ([Clustal-O download and install]
2. Test the local installation using the command-line before run it through php
3. Examine ClustalO help to determine the options to include.
4. Prepare the web application. You use the Blast execution from PDBBrowser example as guideline.
5. Test and complete the local application
6. Copy the scripts to your space on the server (or use a git repo). Adapt the details of the installation as needed, and test.
7. If flask/python is required, let me know

Design a Data Model

You are the manager of a hospital clinical trials support service and need to build a database to manage data (taken from a real case)..

Data Model should cover:

Clinical Study name, and description, contact, laboratory in charge

Application users and roles. We expect a general admin, a supervisor, and people in charge of introducing data.

Pseudonimized study participants (i.e. participants study ids are generated automatically, and should be kept seperated from personal data like names or ids due to legal restrictions, a separated table linking study ids and patient identity should be defined, but it would be stored in a different database).

Clinical Data. Composed by single data items (i.e. age, blood presure, etc), and data files (i.e images, sequencing data). Since the database should server several trials, the identification (label) of the stored data cannot be static, although should be part of a known set of variables. Some of the clinical data is longitudinal, i.e is is obtained along time in a series of visits to the hospital, all data and the corresponding visit dates should be stored.