Freemind Latex Plugin Installation

If you want to display latex formulas on your Freemind mindmap, here are the instructions:

1. Find your freemind dir (/usr/share/freemind)
2. sudo mkdir /usr/share/freemind/plugins/latexmath
3. Checkout/Download https://github.com/Alxa/LaTeXMath-Freemind-Plugin/
4. Read: https://github.com/Alxa/LaTeXMath-Freemind-Plugin/blob/master/INSTALL
5. sudo cp fm-plugin-latexmath/src/main/resources/LaTeXMath.xml /usr/share/freemind/plugins/
6. sudo apt-get install maven2; cd fm-plugin-latexmath; mvn package
7. See and copy jar file in target folder. sudo cp fm-plugin-latexmath-* /usr/share/freemind/plugins/latexmath/
8. sudo cp ~/.m2/repository/net/sf/alxa/jlatexmath/0.9.3-SNAPSHOT/*jar /usr/share/freemind/plugins/latexmath/jlatexmath.jar

Start freemind and you'll see Insert->Latex Equation option.

Note that this does not insert the equation into the branch, but inserts below it and it's a little large.Sample below:

Latex and Bibtex

Using bibliography in latex might be headache sometimes. While I was writing my MSc thesis, I had taken some notes. I'd like to share them with you.

For a while, I was wondering what is the difference between bib and bbl. I learned that when you execute bibtex, bib files are converted to bbl.

Steps for running BIBTEX with LaTEX

1. Run LaTEX, which generates a list of \cite references in its auxiliary file, .aux.
2. Run BIBTEX, which reads the auxiliary file, looks up the references in a database
(one or more .bib files, and then writes a file (the .bbl file) containing the formatted
references according to the format specified in the style file (the .bst file). Warning
and error messages are written to the log file (the .blg file). It should be noted that
BIBTEX never reads the original LaTEX source file.
3. Run LaTEX again, which now reads the .bbl reference file.
4. Run LaTEX a third time, resolving all references.

Uploading on sourceforge

Today, we're trying to publish our project Robinviz. It'll be a 1.0-beta version seperately for windows/linux source/binary. Binary files are around 400MB so it's a bit hard to upload it. Google Code -which we use for project management- limits the maximum file size for uploads. So we had to switch to sourceforge. But uploading on http was still a problem. So I found this solution: Rsync over SSH

At first, I found it hard to understand the URL format but then understood and wanted to share it with you. With the following command, I was able to send my 400MB file with resume support:

rsync -avP -e ssh robinviz-1.0-beta-linux-binary.tar.gz aladagemre,robinviz@frs.sourceforge.net:/home/frs/project/r/ro/robinviz/linux-1.0-beta

robinviz-1.0-beta-linux-binary.tar.gz: filename
aladagemre: username on sourceforge
robinviz: project name
/r/ro/robinviz: the first letter, the first two letters and all letters of the project joined by /
linux-1.0-beta: the folder I'd like to put my file in.

Hope it's useful.

Spring term finished

The spring term has finished. Courses were pretty time-consuming this semester so I could not focus o n our research as I did last semester. Grades are not available yet but I expect them to be satisfying. I've taken Data Mining, Analysis and Design of Algorithms, Software Engineering courses.

In the data mining project, I worked on Yeast localization of proteins database and did classification&clustering analysis.

In the Software Engineering project, as I told before, I've developed a bus-timetable program JIstanbul which has both mobile and desktop versions with J2SE+Swing and J2ME. My project was selected as the best in the class. Currently, in the mobile version, the program can detect the day and fetch the timetable for that day. In the future, I'm planning to add storing time information, closest bus time, frequently used buses features.

Now I have 1 course and masters-thesis left for the next year. I'll be focusing on Robinviz in these summer days.

RobinViz Paper and School Projects

After releasing RobinViz, I focused on my school projects. I've written a Turkish Flag drawer, Conway's Game of Life and Julia Set Fractals drawer in Java and presented the latter one in the Software Engineering class.

Currently I'm developing an Optimal Binary Search Tree implementation in Python as part of my Algorithms class. I've registered for a github account and I put all my codes there.
On the other hand, I'm working on some edge bundling stuff nowadays as part of my academic work. It's really nice but complicated. I hope I can come by a good solution to our problems in our mind.

I think I'll be fixing some problems of Robinviz in the following months. Our published paper (An integrated model for visualizing biclusters from gene expression data and PPI networks) can be found here.

As part of my Software Engineering project, I'm planning to develop a J2ME application to fetch bus timetables from the Internet and display the closest bus times for you to find the best route without waiting your bus.