DBW – Databases and Web development. 2022-23

 

Simple Examples

• Recover Uniprot data (Id, and basic info) from keywords using Uniprot query facilitites. Prepare a php script that takes a single parameter 'q' containing a text query. Use Uniprot search API. Uniprot search (code)
• Parse a (Multi)FASTA file into id, database, basic info (from headers) and sequence. The application should provide a Web form to introduce either A) a Fasta formatted file (pasted or uploaded), or B) a list of Uniprot Ids. Output should be in tabular form (id, database, SwissProt id, and info). Fasta Parser (codes: parseFasta.html, parseFasta1.php, getFasta.php)

Form management

1. Form Management: Build a HTML form similar to PDBBrowser. On the controller page, print the uploaded data and relevant environment variables.
2. More advanced forms: Build a form similar from above, but generating some fields (Experiment type or compound type) from the information hold in the PDB database.
3. Session management: Modify the above form and controller page to remember the inserted data. Consider including error messages from form validation.
4. On-the-fly Form validation: Basic javascript to validate form input. Check for mandatory fields or formats.

Database browser

1. Generate a form with some fields available in the PDB database. In the controller script build an SQL query and generate the output list.
2. Complete the above with paginated output and column ordering.