Software Applications

Bachelor in Genomics - A.Y. 2018/2019

Group photo

Textbook

Ian Sommerville. Software Engineering, 10th Edition. Pearson

Classes

Tuesday and Wednesday from 14:00 to 16:00 - AULA C at ground floor, via della Beverara 123 Bologna

Some exceptions might occur, i.e. check the timetable.

Communication channels

  • Teacher's e-mail: andrea [dot] nuzzolese2 [at] unibo [dot] it
  • Social platform: Facebook group

Exams and project discussion

The agenda for Students' talks on January 15th-16th is available.
  • 04/02/2019 from 9:00am at Aula C via della Beverara 123/2
    • Registration opens on 09/01/2019
    • Registration closes on 03/02/2019
    • Project submission due by 28/01/2019. Submit the project to teacher's email.
  • 18/02/2019 from 9:00am at Aula C via della Beverara 123/2
    • Registration opens on 05/02/2019
    • Registration closes on 17/02/2019
    • Project submission due by 11/02/2019. Submit the project to teacher's email.
  • 28/02/2019 from 9:00am at Aula C via della Beverara 123/2
    • Registration opens on 19/02/2019
    • Registration closes on 27/02/2019
    • Project submission due by 21/02/2019. Submit the project to teacher's email.
  • 11/07/2019 from 9:00am at Room 11 via Zamboni 32
    • Registration opens on 19/06/2019
    • Registration closes on 09/07/2019
    • Project submission due by 09/07/2019. Submit the project to teacher's email.
  • 25/07/2019 from 9:00am at Room 11 via Zamboni 32
    • Registration opens on 12/07/2019
    • Registration closes on 23/07/2019
    • Project submission due by 23/07/2019. Submit the project to teacher's email.
  • 20/09/2019 from 9:00am at Room 11 via Zamboni 32
    • Registration opens on 02/09/2019
    • Registration closes on 18/09/2019
    • Project submission due by 18/09/2019. Submit the project to teacher's email.
Use AlmaEsami for signing up for the exam.

GitHub Code repository

The code repository is meant to provide reusable snippets of Python code that can be directly imported/extended into the implementation of student projects.

The code repository is publicly available on GitHub.

Papers for student talks

  • Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., ... & Hornik, K. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome biology, 5(10), R80. PDF
  • Darriba, D., Flouri, T., & Stamatakis, A. (2018). The state of software for evolutionary biology. Molecular biology and evolution, 35(5), 1037-1046. PDF
  • Russell, P. H., Johnson, R. L., Ananthan, S., Harnke, B., & Carlson, N. E. (2018). A large-scale analysis of bioinformatics code on GitHub. bioRxiv, 321919. PDF
  • Duck, G., Nenadic, G., Filannino, M., Brass, A., Robertson, D. L., & Stevens, R. (2016). A survey of bioinformatics database and software usage through mining the literature. PloS one, 11(6), e0157989. PDF
  • Whetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C., Tudorache, T., & Musen, M. A. (2011). BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic acids research, 39(suppl_2), W541-W545. PDF
  • Cerami, E. G., Bader, G. D., Gross, B. E., & Sander, C. (2006). cPath: open source software for collecting, storing, and querying biological pathways. BMC bioinformatics, 7(1), 497. PDF
  • Lee, T. J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D. W., Tenenbaum, J. D., & Karp, P. D. (2006). BioWarehouse: a bioinformatics database warehouse toolkit. BMC bioinformatics, 7(1), 170. PDF