• 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 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.

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.

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.

• 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.

A link to the report has been placed on the front page of the NMPDR Development Blog under the title Latest Version Database Report so that it can be found easily when it is needed.

• Adding an XML download format.
• Reinstalling the FASTA download format for feature-based searches.
• Fixing the Drug Search. This is not a search for drug targets, but rather a report on the docking results we already have.

There was a bug in the pattern search because the formatter was removing spaces from the pattern string. This has been fixed.

I am currently running the difference report. I added coupling and BBH statistics, both of which have slowed the report considerably, which is why it is still going on. Since this report is not run very frequently, I don't consider that a big problem. Once the report is done, the data will appear here.

This weekend I will re-run the attribute report, which will give me the information I need to begin implementing a drug target search (as opposed to a docking result report). I don't wan to start the attribute report until the difference report is finished.

Finally, I am meeting with Ross on Monday to discuss implementing a close-strain comparison tool. This has become a little more urgent because one of the site users requested it.

I am currently working on the code that allows the user to decide which ID (uniprot, locus tag, etc.) should be displayed in the results. Once that's done, I will fold it into the display code for the various feature searches as part of getting them fixed and adding rollover hints to the search forms. (This is all based on a discussion with Folker and Liz last week.) In the meantime, I am running an attribute report to find out which attributes can be added to the searching. Once that's done, I will need to reload the feature table to get the new attributes, at which point the site will be mostly working except for the help pages and stuff.

In the meantime, the latest attribute report is no available here. For NMPDR core organisms, we have 92% coverage on CELLO data and 50% coverage on TMPRED, which is much better than we had in the previous report.

There are also numerous search problems which result from the search code being in an incomplete state at the time I started the load. I will get back to the search fixes as soon as I finish doing the laundry.