Final Release

The final release of our product. Added some extra functionalities and fixed some bugs. You can now do the following things:

• Click on a node in the graph to get its' content.
• Hover over a genome in the phylogeny to see metadata about that genome.
• Hover over annotations to get the name.
• Added "about" tab.
• Fixed annotation scale
• Fixed certain graph edges missing.

Update: the DNALab-9.0-Demonstration.zip has been added. It is the same as DNALab-9.0.zip except it contains a jar using the TB10 dataset as default. It works smoother than the TB328 dataset due to the size difference and can be used to quickly try out all features.

DNA Lab 8.0

In this release, we have implemented SNP and indel highlighting in the gui. We have also fixed the coloring of the ribbon view. We have also managed to get the 328 genomes data set to work. However, preprocessing takes a considerable amount of time which we weren't able to reduce. For that reason, we include the preprocessed 328 genomes database in the release.

Due to some last minute issues, we've added 2 seperate jars to the zip where different functionalities are working. Version 8.0.1 contains working SNP/indel highlighting, correct width and coloring of the edges and an improved loading screen. Version 8.0.2 is a version that works with the TB328 data set, but does not have correct coloring or SNP/indel highlighting.

Update: there was a folder missing in the zip. It has been added and the jars should run now.

DNA Lab 7.0

Features added:
-Bubble collapsing
-Ribbon view and graph view were merged
-Interaction between graph and phylogenetic tree
-Colours added to ribbon view

The zip contains 2 versions this week. In version 7.0.1, the coloring and phylogeny link work correctly. In 7.0.2, this does not work correctly, but the switching to the graph works correctly when zooming. We've added both so you can see both. In the future, we will of course merge this into one product.

Please be patient with the program, even if it seems to hang, we still have to improve the speed and the feedback to the progress bar of the underlying process.

Playbook Release

This release includes the executable jar file and the pdf file that can be used as a playbook during a presentation. Jar is not runnable from within the rar, please extract it into it's own folder.

DNA Lab 6.0

Some new features:
-Phylogenetic tree is coloured according to lineage.
-Selections in phylogenetic tree can be made gui-wise, there it does not yet interact with the graph.
-Annotations have been added.

DNA Lab 5.0

In this release we've added semantic zoom and improved the phylogeny and graph views. Like before, to run you should extract the zip and run the jar file using java -jar DNALab-5.0.jar

Release version 4 of DNA Lab

In this version we implemented a toolbar so that you can easily load in new .gfa files or revisualize .gfa files that have already been parsed into the database. We also implemented dynamic sizing or our nodes so that if a node represents a large number of nucleotides, it will be bigger than a node with only one.

To run the jar file, simply extract the zip file and run using 'java -jar DNALab-4.0.jar'

TWS Release week 3

The jar is packaged within a zip including pregenerated databases, like previous week. To run, first extract the zip file and then run the jar file.

TWS release week 2

Version 2 of our product. In this release, data about the genomes is already pre-calculated and stored in the database. Therefore, launch doesn't take 2 minutes every times, but only the first time. We already packed the database (in the db folder) with our release, so it should launch quickly every time.

Also, the structure of our project is way cleaner, making the understandibility of the code way better.

First release

A first version of the genome analyzer tool. The tool represents the 10 genomes on the screen, which you can do basic zooming on it.

The data is already stored in a database. We made a parser for this, we already pre-calculated it. This file is also in the release.

The zip-file contains 2 files: A jar-file and a db-folder. Make sure the jar-file and the db-folder are in the same directory. It will take approximately 5 minutes to make something show up on screen.