NMPDR Development Blog

• Data Load. The new NMPDR data is now fully loaded, and we show features in subsystems for all of the new organism groups. The difference report is here. The report shows what has changed in each of the core organism groups, the new and deleted subsystems, the new and deleted organisms, and the statistics used on our semi-annual reports. In addition, it flags unusual situations. In this case, there were 16 organisms without BBHs. Bob is currently fixing them.
• Performance. It takes about 3 seconds to display a protein page. The SEED viewer genome browser takes about 8 seconds. This is comparable to the performance of GBrowse on both the Mirror system (which is the same server as the new version) and the Live system. There has been some concern about the SEED viewer performance, but during the weekend I was running the difference report, which would have slowed things down considerably.
• Functionality. We were having problems with Image::Magick, but this is now fixed. The plan is for Tobi and I to stress-test the viewer this afternoon and fix any problems we find.
• Schedule. The current plan is to stage the new NMPDR on Wednesday the 28th after the programmers' meeting, then roll it over on November 30. If any problems occur, we will roll over on a later date and change the front page to reflect the new information.

Version 22 of the NMPDR has been created on the New Development Server at http://anno-2.nmpdr.org/next/. Note that at this time, no data has been loaded into the databases. The intent is to bring the Sprout database one step closer to looking like a PPO database before we load it.

Two fixes have been slipstreamed into the production NMPDR.

• The hit locations in the context view now show up as gray instead of bright green. To see this, click here and then select the Context button for the first search result.
• The drug targets pages were not displaying any results because the drug target data files had not been copied over to the production server. This has been fixed. Click here to see the results.

The next step is to start setting up version 22 on the new development server.

I have been in the process of setting up anno-2.nmpdr.org as the new NMPDR development server. This is a faster server, and nmpdr-1 is slated for some different sort of thing that I don't fully understand. For a while, things will be a little crazy as I sort out which links point to where.

NMPDR version 21 is officially live. In addition, I have added SOPs to the development wiki for staging an NMPDR for testing, propagating corrections to the staged site, and rolling over a new version.

I will probably not be able to come in on Monday as that is the day the plumbers are coming to pump the water out from the basement and fix the damage.

• The output from the BLAST search is now sorted correctly. Some genes weren't being correctly identified as NMPDR core genes, causing them to float to the bottom of the list.
• The context button on the BLAST/Scan result page has been moved after the NMPDR button.
• The old favored-alias feature has been restored. In addition, when the selected ID type is not FIG, the FIG ID is shown in the organism name column in the familiar old square brackets.
• The formlets on the search output have been changed to fake buttons. This allows users to right-click on the buttons and open the linked pages in another tab or window.

I believe this covers the NMPDR-specific issues Leslie had with version 21. The remaining issues deal with the protein page and will be addressed separately.

The context view available from the BLAST/Scan search now includes additional explanatory text at the top. The pop-up box you get from clicking on a gene now shows only the NMPDR protein page. I am awaiting a response from Toby and Daniel as to whether I can get the click to go directly to the page without the intervening popup box.

When the incoming search pattern or sequence is more than 30 characters, the context view displays a character count rather than the entire sequence, because a long sequence looks really ugly.

I am in the process of re-doing the search helps and converting them to pages in the Seed Wiki. Clicking on the new-fangled blue-question-mark-things will pop up the relevant Wiki page.

In addition to the Wiki conversion, I have 11 more change requests from Leslie and 9 requests from Folker and Liz. Given that the Wiki conversion is essential and I also have to update some of the cover pages myself due to Leslie's absence, I am seriously thinking of pushing ahead the release date by another week or two. I will decide this tomorrow morning based on how much pain I'm in when I wake up.

The NMPDR Viewer now allows downloading each of the three result trees from a metabolic reconstruction. The downloads are done direct-to-disk, like the downloads from the NMPDR search results page.

This was implemented as a response to a customer requirement for the RAST Server. The next step is to move the code over to the RAST server itself.

Version 21 is now considered stable enough for testing. Among the new features that will be available in this release are:

• BlastN, DNA Scan, and Protein Scan are now available on the Tool search page (which replaces the old BLAST page).
• Search output for the Tool Search page contains more information (including the matching sequence for scans and the alignment for BLAST). Each row includes a link to a compare-region display.
• It is now possible to download search results in XML format.
• The search results use real buttons instead of fake buttons simulated using styles. The buttons are automatically converted to URLs when the results are downloaded in XML or tab-delimited format.
• You can specify the type of ID to be used when displaying feature IDs in search results. If a feature does not have an ID of the specified type, it will fall back to the FIG ID.
• Coloring is available on new-style subsystem diagrams.
• The numbers required for the semi-annual report will now automatically be generated as part of the version change process.

There was also a major upgrade to the underlying code for the search. Previously, the search was heavily biased toward searches that return features. Under the new system, the type of result is decoupled from the type of search, which makes it easier to create searches for new types of objects (such as subsystems and genomes) in the future.

The SEED Viewer has been re-activated, and can be found here. There is also a link to it in the sidebar on the front page of the Development Blog. This is the old viewer, and it is currently being used to insure that the NMPDR can support the functions needed by the SEED Viewer. The idea here is that when the new viewer is ready, we will be in a better position to couple it to the rest of the site. In the meantime, because there is no direct link to it on the website, we can test and modify it without disrupting anything on the real web site.

• New Development Site loaded: June 28, 2007
• Latest code and data copied to Staging Site for beta testing: July 25, 2007
• Version 21 published to Public Site: July 27, 2007