This month’s release rolls out additional bugfixes.
A buffer overrun was intermittently causing crashes with using the turbo_button in searches. The fix improves the stability of the turbo_button searches. Again, this feature is still in the experimental stages, thus the ability to disable it is in the parameters file. An additional bugfix corrected cases where the n- and c-terminal modifications of loop-links were being reported elsewhere in the peptide.
A small bug was identified that causes some data corruption with a memory buffer shared by multiple threads. It was tough to replicate because it typically required a lot of modifications on a small dataset with a lot of threads to produce, but it was there nonetheless. The bug has been fixed and Kojak operation returned to normal.
The website was long overdue for some sprucing up. Though I’m not convinced I’ll be happy with it next month, for now it is much easier to look at. Changes to Kojak include a drastic overhaul of how cross-links and mono-links are specified in the parameters. Now it is possible to simply specify the amino acids that can be reacted to each end of the linker. The new syntax is explained in depth in the online parameter documentation. Another new feature is the addition of the turbo_button parameter (0=off, 1=on). It can significantly speed up the peptide search analysis portion of the algorithm. Because I’m testing edge cases for performance, you are allowed to disable the turbo_button if desired. In the future, it may be turned on by default.
The Kojak Spectrum Viewer was also updated to the fifth alpha release (KSV-a5). The major new feature is the ability to export .png images of your results. They appear in the folder of the pepXML file being viewed. It is also possible to increase peak line thickness for easier viewing. Many more visualization improvements are still needed and will be rolled into the next alpha releases. KSV-a5 is packaged with Kojak 1.5.0.
For those that are curious, the circle map featured on the front page was generated using ProXL, a Web application for the management, sharing, and visualization of cross-linked search results from several algorithms (including Kojak, of course). I recommend checking it out. To learn more, visit the ProXL site or read the publication.
The Linux release of Kojak 1.4.3 has been posted. It includes the Kojak Spectrum Viewer as well. However, some support libraries may need to be installed first. These are detailed in the instructions page for the Viewer. The viewer is also being regularly updated while in alpha stage. To obtain the latest build, follow the download links on the Viewer page. The pre-packaged viewer with Kojak will not be updated until the next Kojak release.
Two major announcements today. First, I am releasing the Kojak Spectrum Viewer. It is a windowed application for viewing Kojak search results. Specifically, the Kojak results need to be formatted in PepXML. More on this down below. The viewer actually accepts search results from any algorithm formatted in PepXML, so feel free to use it with whatever you want to visualize. Right now the software is somewhere between alpha and beta stages, so a few features are in flux, and an occassional bug might rear its head. Documentation is very sparse, but a few details can be found on the Viewer tab at the top of the page. The viewer is packaged with the latest release of Kojak (1.4.3), or available as standalone.
The second announcement is the release of Kojak 1.4.3. There are a few bug fixes, but most importantly, you can now export results in PepXML. To do so, simply set export_pepxml = 1 in your configuration file. Exporting results in pepXML is critical for using the Kojak Spectrum Viewer to visualize your results. Also, due to limited time, I’m postponing the Linux release. Don’t worry, it will be posted soon.