Exercise 'Protein Prediction II' for Computer Scientists
Welcome to our main information exchange for the exercise 'Protein Prediction II' for Computer Scientists!
The organization, requirements and grading of the exercise are explained here by the mentors. All students will have one log in account and may add content to this wiki. The students are encouraged to add in their opinion useful links or other material to the wiki page and design the class together with us.
The exercise grade accounts for 60% of the final lecture grade. The grading will be based on your short 5 minutes bi-weekly presentation of your progress during the coding phase, the resulted visualization component that you will develop during the exercise, its clear and complete documentation, and the final 10 minutes presentation of the component to the group including Prof. Rost.
The mentors for the exercises will be:
- Juan Miquel Cejuela - a PhD student at RostLab, text mining expert and functional programming languages enthusiast. Also creator of tagtog.net
Our exercises will heavily benefit from the expertise and enthusiasm of:
- Sebastian Wilzbach - a Bioinformatics student at Rostlab and a former GSoC student. Enthusiast of NodeJS and CoffeeScript.
- David Dao - an Informatics Student at TUM interested in interactive visualization, data mining and evolutionary Bioinformatics. Also a former GSoC student
One of the biggest breakthroughs in life sciences has been the ability to sequence the genetic code of life - the DNA. As the sequencing techniques become cheaper and faster, the amount of biological data stored in our databases is increasing every day. The data does not come from sequencing experiments only, but also from many other technologies that are used to understand organisms and diseases at the systems level. It a challenge nowadays to integrate the variety of data in a meaningful and research facilitating way.
Schedule & Notes
|16 Oct||Introduction to BioJS (Guest lecturer: Dr. Manuel Corpas) & HTML||Slides - Intro to the exercise |
Slides - Intro to web development
BioJS Article Collection
|30 Oct||Introduction to Interactive Visualization with D3||D3 Website |
Slides - Recap and Intro to D3
|06 Nov||Visualization Principles & Best Practice||Nice git app |
|13 Nov||Project Proposals||Project ideas |
Tips for your blueprint
|20 Nov||Supervised Team Meeting, Intro into BioJS||Intro to BioJS|
|27 Nov||Open Questions Session, Intro to Node.js and Tips for Development||Modular JS |
|05 Dec||Open Hackathon (whole day! & with supervisors & pizza/drinks ? )|
|11 Dec||Supervised Team Meeting & Presentation of Progress||Homework 6|
|18 Dec||No Exercise|
|03 Jan||Open Hackathon (starts at noon 12:00 & with supervisors & drinks/snacks )|
|08 Jan||Final Project Presentation (Prof. Rost) and Exercise afterwards!||Live examples |
Slides Integration into BioJS
|25 Jan||Deadline for Documentation and Submission to BioJS|
We encourage the students to retain from contacting the mentors by email. Instead please use the opportunity to talk to us during the exercise or use the PP2 CS 2014 mailing list. Feel free to post any question you might have concerning organizational or technical aspects of the exercise. The mentors will keep an eye on the mailing list but would expect (where possible) the students to help each other reciprocally.
D3 - Interactive Data Visualization for the Web, Scott Murray, O’Reilly (2013) Free online version
We listed a tons of Resources you can use for your project! This list can be extended by you :)
- Online schools