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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 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. |
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− | + | = Grading = |
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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 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. |
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− | + | = Mentors = |
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The mentors for the exercises will be: |
The mentors for the exercises will be: |
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* [https://github.com/daviddao David Dao] - an Informatics Student at TUM interested in interactive visualization, data mining and evolutionary Bioinformatics. Also a former [https://vimeo.com/103800680 GSoC] student |
* [https://github.com/daviddao David Dao] - an Informatics Student at TUM interested in interactive visualization, data mining and evolutionary Bioinformatics. Also a former [https://vimeo.com/103800680 GSoC] student |
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− | + | = Project description = |
|
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. |
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. |
||
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The visualization plays a crucial role in the ability of interpreting the data and focusing on those details that shed light on specific hypotheses. The complexity of the data we are facing in modern life sciences requires more advances technologies than the usual static HTML pages when accessing them. They require dynamic visualization tools that allow real-time interactions. JavaScript is a language of modern browsers and thus is perfect for developing client-side browser-based tools. In the exercises of this semester we will build tools for the visualization of biological data on the web from scratch and share those with the community! |
The visualization plays a crucial role in the ability of interpreting the data and focusing on those details that shed light on specific hypotheses. The complexity of the data we are facing in modern life sciences requires more advances technologies than the usual static HTML pages when accessing them. They require dynamic visualization tools that allow real-time interactions. JavaScript is a language of modern browsers and thus is perfect for developing client-side browser-based tools. In the exercises of this semester we will build tools for the visualization of biological data on the web from scratch and share those with the community! |
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− | + | = Schedule & Notes = |
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<div style=" text-align:left; width: 60% ; overflor:auto; height:10em border:2px"> |
<div style=" text-align:left; width: 60% ; overflor:auto; height:10em border:2px"> |
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| 16 Oct || Introduction to BioJS (Guest lecturer: Dr. Manuel Corpas) & HTML || [http://pp2-ex.github.io/ex1-intro/ Slides - Intro to the exercise] <br> [http://pp2-ex.github.io/webdev-intro/#/ Slides - Intro to web development] <br> [http://f1000research.com/article-collections/BioJS BioJS Article Collection] <br>[[Homework 1]] |
| 16 Oct || Introduction to BioJS (Guest lecturer: Dr. Manuel Corpas) & HTML || [http://pp2-ex.github.io/ex1-intro/ Slides - Intro to the exercise] <br> [http://pp2-ex.github.io/webdev-intro/#/ Slides - Intro to web development] <br> [http://f1000research.com/article-collections/BioJS BioJS Article Collection] <br>[[Homework 1]] |
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|- |
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− | | 23 Oct || Technology Fundamentals (HTML, CSS, SVG, Git(Hub), JavaScript) || |
+ | | 23 Oct || Technology Fundamentals (HTML, CSS, SVG, Git(Hub), JavaScript) || [https://pp2-ex.github.io/webdev-js Slides - JavaScript: The bad parts ] <br> [[Homework 2]] |
+ | |- |
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+ | | 30 Oct || Introduction to Interactive Visualization with D3 || [http://d3js.org/ D3 Website] <br> [http://pp2-ex.github.io/intro-to-d3/ Slides - Recap and Intro to D3] <br> [[Homework 3]] |
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+ | | 06 Nov || Visualization Principles & Best Practice || [http://www.sourcetreeapp.com/ Nice git app] <br> [https://i12r-studfilesrv.informatik.tu-muenchen.de/pp22014/index.php/Homework_4 Homework4] |
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− | | 30 Oct || Introduction to Interactive Visualization with D3 || |
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− | | |
+ | | 13 Nov || Project Proposals || [[Project ideas]] <br> [[Tips for your blueprint]] <br> [[Homework 5]] |
|- |
|- |
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+ | | 20 Nov || Supervised Team Meeting, Intro into BioJS || [https://docs.google.com/presentation/d/19B9m4FuQvwMc1UHD9-VCY143w4GQ7C84ObeDex6vVsQ/present Intro to BioJS] |
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− | | 13 Nov || Project Proposals || |
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|- |
|- |
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+ | | 27 Nov || Open Questions Session, Intro to Node.js and Tips for Development || [http://pp2-ex.github.io/modular-js/#/ Modular JS] <br> [https://github.com/pp2-ex/modular-js Live Coding] <br> [http://anvaka.github.io/allnpmviz3d/# NPM Visualization] |
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− | | 20 Nov || Supervised Team Meeting || |
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|- |
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− | | |
+ | | 05 Dec || Open Hackathon (whole day! & with supervisors & pizza/drinks ? ) || |
|- |
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− | | |
+ | | 11 Dec || Supervised Team Meeting & Presentation of Progress || [[Homework 6]] |
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− | | |
+ | | 18 Dec || '''No Exercise''' || |
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|- |
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− | | |
+ | | 03 Jan || Open Hackathon (starts at noon 12:00 & with supervisors & drinks/snacks ) || |
+ | |- |
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+ | | 08 Jan || Final Project Presentation (Prof. Rost) and Exercise afterwards! || [[Live examples]] <br> [http://slides.com/daviddao/js-best-practices-12/ Slides Integration into BioJS] |
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+ | |- |
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+ | | 25 Jan || Deadline for Documentation and Submission to BioJS || [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003453 10 Rules to write a paper] |
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|} |
|} |
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</div> |
</div> |
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− | + | = Contact = |
|
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 [https://groups.google.com/forum/#!forum/pp2-cs-2014 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. |
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 [https://groups.google.com/forum/#!forum/pp2-cs-2014 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. |
||
− | + | = Recommended Readings = |
|
[[File:scott.jpg | right]] |
[[File:scott.jpg | right]] |
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''D3 - Interactive Data Visualization for the Web'', Scott Murray, O’Reilly (2013) [http://chimera.labs.oreilly.com/books/1230000000345 Free online version ] |
''D3 - Interactive Data Visualization for the Web'', Scott Murray, O’Reilly (2013) [http://chimera.labs.oreilly.com/books/1230000000345 Free online version ] |
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+ | = Resources = |
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− | '' JavaScript Garden [http://bonsaiden.github.com/JavaScript-Garden/ open source + online ] |
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+ | We listed a tons of [[Resources]] you can use for your project! This list can be extended by you :) |
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+ | = Related courses = |
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− | '' JavaScript: The Good Parts, Douglas Crockford, O’Reilly (2013) [http://www.amazon.com/JavaScript-Good-Parts-Douglas-Crockford/dp/0596517742 Amazon] |
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+ | * [http://nesterko.com/lectures/stat221-2012/lecture1/#/ Harvard Stat 221] |
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− | == Resources == |
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+ | * [http://courses.cs.washington.edu/courses/cse512/14wi/ Washington CSE512] |
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+ | * [https://github.com/advanced-js/syllabus Advanced JS] |
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+ | ;Online schools |
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− | === JavaScript === |
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− | * [https://developer.mozilla.org/en-US/docs/Web/HTML Mozilla] |
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− | * [http://www.html5rocks.com/en/resources HTML5rocks] |
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− | * [https://google-styleguide.googlecode.com/svn/trunk/javascriptguide.xml Google JavaScript Style Guide] |
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− | * [https://bonsaiden.github.io/JavaScript-Garden/ Functional JS Garden] |
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− | * [https://www.npmjs.org/doc/misc/npm-coding-style.html NPM style guide] |
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− | * [https://github.com/rwaldron/idiomatic.js Principles of Writing Consistent, Idiomatic JavaScript] |
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− | * [https://github.com/advanced-js/syllabus Advanced JS] |
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* [http://www.codecademy.com/en/tracks/javascript Codecademy JS] |
* [http://www.codecademy.com/en/tracks/javascript Codecademy JS] |
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+ | * [https://www.codeschool.com/courses/javascript-road-trip-part-1 Codeschool JS Part1], [https://www.codeschool.com/courses/javascript-road-trip-part-2 Part2], [https://www.codeschool.com/courses/javascript-road-trip-part-3 Part3] |
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− | ;OO JS |
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+ | * [https://www.codeschool.com/courses/javascript-best-practices Codeschool JS best practices] |
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− | * [https://developer.mozilla.org/en-US/docs/Web/JavaScript/Introduction_to_Object-Oriented_JavaScript Mozilla's Intro to OO-JS] |
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− | *Codeschool |
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− | :* [https://www.codeschool.com/courses/javascript-road-trip-part-1 JS Part1] |
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− | :* [https://www.codeschool.com/courses/javascript-road-trip-part-2 JS Part2] |
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− | :* [https://www.codeschool.com/courses/javascript-road-trip-part-3 JS Part3] |
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− | :* [https://www.codeschool.com/courses/javascript-best-practices JS best practices] |
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− | ; High-perf JS |
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− | * [http://www.smashingmagazine.com/2012/11/05/writing-fast-memory-efficient-javascript/ Writing Fast, Memory-Efficient JavaScript] |
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− | * [https://developers.google.com/speed/articles/javascript-dom out-of-dom operations] |
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− | |||
− | === Git & Github === |
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− | |||
− | ; Git |
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− | * Git [https://rogerdudler.github.io/git-guide/ Guide] |
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− | * [https://try.github.io Tutorial] |
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− | * [http://gitref.org/ Reference] |
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− | * [http://git-scm.com/ official website] |
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− | ;Github |
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− | * [http://www.thinkful.com/learn/a-guide-to-using-github-pages/ Guide to Github pages] |
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− | * [https://pages.github.com/ Official site] |
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− | |||
− | === HTML & CSS === |
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− | * [http://www.codecademy.com/en/tracks/web Codecademy HTML] |
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− | * [https://www.codeschool.com/courses/front-end-formations Codeschool Frontend] |
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− | * [https://www.codeschool.com/courses/css-cross-country Codeschool CSS Country] |
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− | |||
− | == Related courses == |
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− | |||
− | * [http://nesterko.com/lectures/stat221-2012/lecture1/#/ Harvard Stat 221] |
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− | * [http://courses.cs.washington.edu/courses/cse512/14wi/ Washington CSE512] |
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− | + | = Contests = |
|
* [http://biovis.net/year/2014/info/contest_data BioVis] |
* [http://biovis.net/year/2014/info/contest_data BioVis] |
Latest revision as of 12:29, 15 January 2015
Contents
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.
Grading
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.
Mentors
The mentors for the exercises will be:
- Tatyana Goldberg - a PhD student at RostLab and a former org admin and mentor of a JavaScript project in the Google Summer of Code (GSoC) Program
- 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
Project description
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.
The visualization plays a crucial role in the ability of interpreting the data and focusing on those details that shed light on specific hypotheses. The complexity of the data we are facing in modern life sciences requires more advances technologies than the usual static HTML pages when accessing them. They require dynamic visualization tools that allow real-time interactions. JavaScript is a language of modern browsers and thus is perfect for developing client-side browser-based tools. In the exercises of this semester we will build tools for the visualization of biological data on the web from scratch and share those with the community!
Schedule & Notes
Date | Topic | Links |
---|---|---|
16 Oct | Introduction to BioJS (Guest lecturer: Dr. Manuel Corpas) & HTML | Slides - Intro to the exercise Slides - Intro to web development BioJS Article Collection Homework 1 |
23 Oct | Technology Fundamentals (HTML, CSS, SVG, Git(Hub), JavaScript) | Slides - JavaScript: The bad parts Homework 2 |
30 Oct | Introduction to Interactive Visualization with D3 | D3 Website Slides - Recap and Intro to D3 Homework 3 |
06 Nov | Visualization Principles & Best Practice | Nice git app Homework4 |
13 Nov | Project Proposals | Project ideas Tips for your blueprint Homework 5 |
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 Live Coding NPM Visualization |
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 | 10 Rules to write a paper |
Contact
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.
Recommended Readings
D3 - Interactive Data Visualization for the Web, Scott Murray, O’Reilly (2013) Free online version
Resources
We listed a tons of Resources you can use for your project! This list can be extended by you :)
Related courses
- Online schools