Last weekly update

I've just uploaded my code that I'll be evaluated for Summer of Code experience (version 2.2.2). Whew! I really enjoyed the summer and learned a lot. There still are many more features I'd like to add, but I feel pretty happy about the product at this stage.

Thanks, everyone!

Weekly update

I've spent most of the week tying my pages together. Now the user can input haplotype group data as well as the basic input data. Also, the edit data page now integrates with the rest of the site. The color picker that dynamically updates the pie wedge colors has been tested as well.

Things to do this week:

• Clean up code for repository.
• Include comments on the license, etc.
• Get code into repository.
• Write documentation and user instructions.
• Edit CSS and make site look prettier.
• Prepare presentation for NESCent meet-up at the end of the week.

Weekly update

This week I've spent hacking away at the data management page. I've got all (cross you fingers) the bugs smoothed out from transferring the changed data from the data management page to the viewer page. A new feature of note is that the program now sorts the haplotypes by groups and the user can color all haplotypes in a group at once. (Note, I haven't uploaded the newest version to the website yet, sorry).

Features added this week:

• Can include/exclude haplotypes and populations.
• Can edit data.
• Can specify haplotype groups.
• Can color by haplotype group.
• Changing colors in the colorpicker now changes the associated pie wedge colors in real time.

Next week:

• Meet with David about the remaining goals for the project, and project timeline.
• Update the export function to allow grouping by haplotype groups, etc.
• Tie the data management page to the input data page.
• Update website with latest release.
• Research copyright laws and permissions concerning the maps.

Weekly update

Most of this week has been spent on the include/exclude data and data management feature. It's not quite complete yet. I've run into a lot of difficulty getting the event handlers to update the appropriate javascript variables.

This week I:
Updated the website with a working version (including color picker).
Worked on getting data manager working.

Next week's plan:
Finish data management page.
Start legend/logo export feature.
Look into copyright permissions info from google.

Weekly update

This week I:
1. Got my code into SVN. I feel safer already.
2. Made the input protocol more flexible.
3. Allow users to set own population names.
4. Allow users to change haplotype colors.
5. Updated website.

Next week I will:
1. Update website with new version.
2. Get code into repository.
3. Add grouping of haplotypes feature.
4. Add include/exclude data screen.

Weekly update

Sorry for the lack of posts, I was away at the Botany 2007 conference in Chicago. Things went great at the conference. I managed to get the PhyloGeoViz skeleton mostly working prior to the conference and was able to actually input my own data into the program! It was a great moment. I then created most of my talk's slides based on this output. I pitched the project and NESCent's Phyloinformatics Summer of Code and Google's Summer of Code programs at the end of my talk. Several people approached me afterwards, and they seemed very interested in participating next year! So hopefully I was able to do some recruiting.

On the coding front, I fixed a bad bug that was causing the program to barf in versions of Firefox without the debugger plugin. Unfortunately, the code still doesn't work in Internet Explorer. I also fixed a bug relating to dragging and zooming pies.

To do for this week:

• Catch up on the project blog and chronicle what changes I've made to the code and my bug fixes.
  
• Write function that will output the legend as overlay data in the exported kml.
• Write function that can change the boundaries of the bins for the different pie sizes.
• Write feature so that user can choose whether all the pies are the same size or have relative sizes.
• Write a color picker function for changing the haplotype colors.

Weekly plan

This week is a bit frantic because I leave for the Botany conference on Saturday. I've been making a big push to have PhyloGeoViz ready for an alpha release and debut there. Here's my to do list for this week:

• Transfer homepage style to the other app pages so the look is consistent.
• Figure out export.php bug on server so that it will run!
• Write function that will output the legend as overlay data in the exported kml.
• Write function that can change the boundaries of the bins for the different pie sizes.
• Write feature so that user can choose whether all the pies are the same size or have relative sizes.
• Write a color picker function for changing the haplotype colors.
• Import and manipulate my own data to create slide for talk!!!

Version 0.2 up

Busy, busy week. Version 0.2 is up! I managed to get the export function working. The app can now write a kml file that can be read by Google Earth. This was a bit tricky because I had to fix several functions that weren't updating some of the variables properly after an event changed their state. In any case, that's working now.

I was also able to implement a few new features on the preview page. The pies can now be different sizes based on the population's sample size. The pies can also be increased or decreased in diameter. Also, I can now generate legend data. I'm showing the haplotype labels and their corresponding colors and the sample size to pie diameter legend data.

Weekly update

This past week focused on development of a basic data input page. I decided to use form variables (at least to start with) as the way to pass information between pages. I had to learn how to write the html to allow that plus some php to parse the passed information. I also had to figure out how to pass the variables between php and javascript to get the input data and viewer scripts I'd written to get along. Anyways, as a result I have a rudimentary input page tied to my viewer now. I, of course, still need to clean it up, add error handling, different input types, etc. But it's a start!

On the administrative side of things, I added my project blog to the Planet SoC site. Basically it's a neat aggregation of a bunch of blogs concerning many different Google Summer of Code projects. I also updated the wiki with my design doc.

To do for this week:
Get basic output page written and in synchrony with the other pages.
If time, add some functionality to the viewer (like changing colors).

Weekly update

This past week I:

• Met with David and got feedback on my design document.
• Wrote a map preview app that uses javascript and generates a random pie on a google map that is draggable and zoomable.

Next week's goals:

• Update design document; post it to the wiki.
• Decide on how to pass information from page to page (through form variables, writing/reading a data file, a database server like MySQL).
• Design a data structure to be used.
• Write a simple input page that allows uploading of a data file.
• Link input page to preview page (the pie viewer that was written last week).

Weekly update

This past week I put together a draft of my design document. I tried to be as comprehensive as possible and made some mock ups for each page the user will encounter. Any comments on it are appreciated!

After doing all this design work I realize that I need to learn a lot more javascript than I had expected. While I'll still be exporting KML to Google Earth, I'll be previewing the visualizations a lot more in Google Maps which uses javascript. This puts me a little behind, because I'll have to get caught up on javascript this week too.

To do this week:

• Meet with David and get feedback on design doc.
• Make changes to design doc; post on wiki.
• Familiarize self with javascript fundamentals
• Implement the basic pie chart generation functionality. Functionality should include:
• Draw a pie on a google map.
• Plots multiple objects (working up to pie charts, but starting with placemarks) on a map.
• Basic import of data.
• Basic export to kml.

Weekly update

This past week I...

• Explored Google Earth and its APIs.
• Figured out an algorithm for calculating vertices for drawing "circles" on a map.
• Figured out how to write a pie chart in KML.
• Explored Google Maps APIs.
• Learned some javascript.
• Learned how to embed Google Maps in a web page.
• Have a better idea of what the overall design of the program will be like.

Next week the focus is on fleshing out the application's design. I will...

• Produce a page by page description of what the user sees.
• To do so I will consider:
• How to input data. Are they going to upload files, input in a text box? What format?
• How to export data. Format? Data persistence? Can users store data, results, maps, etc.?
• What is the viewer? Google earth? Google maps?
• How large are the pie charts going to be in comparison with the geography?
  
• How do we deal with the problem of overlapping pie charts?
• How are we going to color the pie charts? What if there are large numbers of haplotypes, how do we color them all distinctly and usefully?
• The results of these decisions will be a comprehensive design document posted on the wiki.

Detailed project plan

Here's my preliminary weekly project plan. Dates refer to the beginning of that work week. Any comments are appreciated!

Now til Start:

• Phase 0: Getting development environment set up
  • Set up homepage, wiki, repositories, etc.

May 28

• Phase 1: Exploratory phase
  • Learn how to embed maps on a webpage.
  • Learn the relationship between Google Earth and Google Maps.
  • How are they the same, how are they different? What can you do with one that you can't do with the other?
  • Explore KML and general XML.
  • Explore Google Earth and Google Maps APIs.
  • Create a pie chart using KML.

June 4

• Finish exploratory work if neccessary.
• Phase 2: Finalize design
  • Page by page description of what the user sees.
  • How to input data. Are they going to upload files, input in a text box? What format?
  • How to export data. Format? Data persistence? Can users store data, results, maps, etc.?
  • What is the viewer? Google earth? Google maps?
  • How large are the pie charts going to be in comparison with the geography? How do we deal with the problem of overlapping pie charts?
  • How are we going to color the pie charts? What if there are large numbers of haplotypes, how do we color them all distinctly and usefully?
  • The results of these decisions will be a comprehensive design document posted on the wiki.

June 11

• Implement the basic pie chart generation functionality. Functionality should include:
  • Basic import of data.
  • Basic KML output writer.
  • Function that draws a pie chart.
  • Function that plots objects (working up to pie charts, but starting with placemarks) on a map.
• Write corresponding documentation.

June 18

• Combine pie chart generation and chart plotting functionality.
• Write the functions that allow adjustments to the output (e.g. changing pie sizes, allowing the user to change haplotype colors, etc).
• Write corresponding documentation.

June 18

• Work on a function that allows the user to move pie charts around spatially (and to save those movements).
• Write corresponding documentation.

June 25

• Write the functions that display the KML back to the browser.
• Write corresponding documentation.

July 2

• Prepare for Botany conference.
• Get code submitted to Google for midterm code check in.
• Get a prototype of the viewer available for download.
• Make sure I'm meeting the midterm evaluation criteria

July 9

• Work on bugs that arose from earlier code.
• Revisit full data manager design. Finalize UI design.

July 16

• Implement UI for the data import functionality.
• Expand (?) data files that are acceptable (haplotype, genotype, etc.)
• Write the corresponding documentation.

July 23

• Implement UI for customizing data analysis.
  • Example: the user should be able to select what loci/alleles/populations to include/exclude in the analyses.

July 30

• Implement UI for output data manipulation.
  • Example: the user should be able to change the relative pie sizes, move pies around, change haplotype colors, etc.

August 6

• Implement functions that allow the user to save the map visualization (e.g. jpg) or to save the KML file.

August 13

• Perform user tests.
• Ensure that the viewer and the data manager are well integrated.
• Deposit code with Google.
• Update website with new product, and all documentation.

August 20

• Done coding. Final evaluations.

Goals for this week

Complete detailed project plan, submit it to David, post on wiki.
Focus on how to generate these KML files:
Install Apache and PHP on laptop.
Investigate PHP.
Investigate java as an alternative.
Set up code repository on google.