Name: Stanisław Robak

Email: stanislaw.robak94@gmail.com

Brief background:
Computer Science sophomore at the AGH University of Science and Technology. Happy to learn new things and willing to do some interesting and valuable project this summer.
I am strongly interested in the fields of Artificial Intelligence, Data Science, Functional Languages.

I like challanges and solving problems, especially algorithmic ones.

At the university I have learned a lot about the Java programinng with some mini projects and one bigger: Java web application with the Spring Framework.
Those are the main technologies which I would like to use in the project.

I love to learn on my own, so i took many courses as my independent coursework.
On the Coursera I have completed online course "Image and video processing: From Mars to Hollywood with a stop at the hospital" which gave me some background in image analysis and provided with an overview of image processing and analysis in medical applications.
From course syllabus: "Week 9 - Medical Imaging: As an example of medical image analysis, we will illustrate examples and techniques in the areas of brain research and virus analysis."
I was also exposed to Data Science and Machine Learning techniques like classification which I might find useful during the project.


Programming interests and strengths:
I like functional programming so I had expierience with languages like Haskell, Scala, Erlang.
But for the purposes of this project more suitable is my experience with Java. I suggest using Spring Framework which I found well suited for doing web applications with it's MVC components.
I plan to make this application well tested. I would like to use JUnit for testing.

I do not have any prior expierience with open source development.

The main thing I would like to achieve is to connect many of my skills and transform them into one useful product.

Interest and Background in biology or bioinformatics:
I generally love science and I am interested in any advances in it. When it comes to biology I especially like genetics.
Last summer I have successfully completed online course: "7.00x Introduction to Biology - The Secret of Life" taught by Eric S. Lander on edX platform. I have gained Honor Code certificate.
I think I have fine background to learn new things in biology. Last summer learning biology was an eye-opening expierience and it would be great to learn more of it this year and connect it with my professional area - Computer Science.

Ideas for a project:
The main idea for the project is described in a simple user story:

As an user I would like to upload a picture of a blood sample and gain knowledge about a probability of a cancer.

Of course application would provide many measurements to let user know about presence and absense of various molecules among other parameters.
The aim of the project is to make it simple.
User should have quick and easy way to upload pictures (for example from mobile devices) and then get desired statistics.

Web application requirements:
* intuitive and easy to use
* robust
* simple
* web-based
* supporting mobile devices

After uploading a picture all core algorithms would take place on the server side. Then the results would be send back to the user.
Core algorithms would be divided in three parts: image preprocessing, detection, measurement.

Web application core requirements:
* highly reliable results
* support loss-less image compression
* extensible for adding new features

Implementation plan:

1. Make simple web application template using Spring MVC framework with some persistance

2. Add uploading of a pictures available

3. Implement image preprocessing algoritms

4. Implement detection algorithms

5. Implement measurements algorithms

6. Transform measurements to the user readable form

7. Make nice statistics/graphs

8. Implement better persistance with samples and results for a given user (user acounts, better support)

Timeline:

25 May - 10 June - point 1 along with designig algorithms for points 3-5

10 June - 26 June - point 2 along with implementing tests for 3-5 (TDD approach) + implementing "draft algorithms"

26 June - 3 July - mid-term evaluation, testing, bug-fixes

3 July - 17 July - points 3-5

18 July - 25 July - point 6

26 July - 1 August - point 7

2 July - 17 August - point 8, testing, fixing bugs

17 August - 28 August - final evaluation

After each point I would test implemented features, but tests would sometimes be written before implementation(TDD).
I would also like to support continuous delivery approach so that always there would be something that works.

Before the mid-term I would like to have working web application with all desired behaviour (uploading pictures, sending something back to the user) and with the accurate description of planned implementation of the core logic.

This is very general timeline, everything can change if mentor suggests so.

Described in the Ideas Page "ImageJ" looks like a very good software, which would be a great source of inspiration for implementing and using image processing algorithms.

The main hurdle is that I would have to learn about cancer detection and implement reliable algorithms using that knowledge. I hope on help from mentor in suggesting some resources for gaining that knowledge (recommending books etc). Implementation of the web application part is not my biggest concern.


Commitment this summer:
My classes at the university finish in the middle of June and I plan to pass all of my exams by the end of that month. But this does not mean that I am not available till that time :)
I do not have any other school-related activities scheduled during the coding period and I do not have a full- or part-time job or internship this summer. If I do not join GSOC I would probably find something to work on but of course I would love to work on this project.
I can approximate that before the end of my university year I can spend at least 15 hours per week. But it is a lower bound, if I do not meet the deadlines in my timeline I would increase that amount (up to the limits of university workload).
After my exams (since the beginning of July) I would increase that amount to about 30-35 hours per week. Possibly with some short break during summer.