Scatter Plots Are Live on CDD!

Just in time for the holiday, we are happy to announce the beta release of a much-requested feature addition to CDD Vault: Scatter Plots.

Before we delve into details, note that we’ve implemented this feature without requiring the installation of additional plug-ins and in a way that works for all supported browsers (and even some unsupported ones).

We want to stress that this is a beta release, meaning that while everything pretty much works, there are a few kinks to be worked out and the performance is not yet where we want.

Scatter plots are accessible from the search page once you have run a query.

Clicking on this link opens a new Plotting & Statistics window. You can open as many of these windows as you like with different results in each one, and each window can be expanded full screen.

For this initial release, we have implemented several useful options including axes selection, series configuration, and display configuration.

It’s possible to zoom in on any region of the plot by mouse selection and view details about any particular point by just hovering the mouse above the point.

At any time you can save the current plot as a PDF, which you can then drag and drop into PowerPoint or Microsoft Word for presentations and reports.

We are actively working on improving the speed of data loading, and with that the number of data points that can be displayed at once. We also plan to allow plotting readouts from one protocol/run against another (we just have to work out what to display when a given batch of a molecule has multiple readout values in a protocol). Down the road, we plan to add more plot types (histograms and box plots). Most of all, however, we want to hear your feedback and suggestions for what would be most valuable.

You can read the full release notes that include other minor fixes and enhancements we work on as an ongoing effort to streamline CDD by logging in.  If you do not have an account and want to see scatter plots for yourself, you can register for a free CDD Public account.

Many of you noticed that CDD was unavailable for much of the day on Thursday, April 9th. We wanted to take a moment to explain in more detail the events that caused this outage, and to alert you to a new resource, http://status.collaborativedrug.com.

Those of you who live in the San Francisco bay area might have heard about the incident that occurred early Thursday morning, in which someone cut fiber communication backbone cables in two locations, one near San Jose and the other in San Carlos, CA. The police are pursuing a criminal investigation for this act that disrupted cell or landline phone service in several areas, including disabling ATMs and even 911 service. AT&T has announced a $250,000 reward for information leading to the conviction of those responsible.

The act also completely cut Internet connectivity to the facility where CDD houses its servers. All of the facility’s customers went offline. CDD’s servers were up and running during the entire incident, and would have serviced your requests the same as always had the facility’s Internet connection not been severed. To the facility’s credit, its staff was able to procure another backbone connection early in the afternoon, restoring complete connectivity around 2pm (the repair on the cut lines was completed late Thursday evening). Prior to Thursday, we had been very happy with our experience at the facility and with its staff, with no prior power or network interruptions. CDD is following up with the vendor to understand why their redundant connections to the Internet did not protect them from this failure. Please be assured that we hold our hosting vendors to high standards.

CDD’s uptime has been outstanding for an organization of its size. That said, Thursday’s incident made it clear that one area we could do better is in keeping our customers informed in the event of an extremely rare occurrence like this. As a result, we are in the process of setting up http://status.collaborativedrug.com as a place customers can go for status updates in the event that CDD goes down. This website is hosted at a separate facility in Europe, so any calamity that can be imagined would not cause both CDD’s main servers and http://status.collaborativedrug.com to go offline at the same time. We also plan to include a link to an independent third-party measurement of CDD’s uptime, so that we can prove how outstanding our uptime usually is.

Last evening we released the latest update to CDD, customizable mine results. This release makes it easy to add (or remove) protocols, readouts, molecule synonyms and/or user-defined fields to/from your mine results, allowing you to customize the displayed data to be most relevant. To access this new feature, perform a mine query, then click the new “Select data to display” link on the right above the search results table:

Once you click this link, a panel will open, allowing you to select which protocols, readouts, chemical properties, or molecule fields you want to view (or not view). Clicking and dragging the green four-way arrows reorders the various sections.

The list of Molecule Fields includes molecule synonyms, all user-defined fields in your private group, and all published user-defined fields associated with any of the publicly or privately-shared data sets you’ve selected in the Collaborate Data Sets tab.

One feature we did not provide in this release is a way to save these display preferences. We’d like feedback on what would be most useful here. We have had a couple ideas:

1. Save the display options with a saved query, so that next time you run the query, the sections you selected will be displayed in the same order.
2. Save the display options for each section so that the next time you perform any search, those sections will have the same readouts/properties/fields displayed. Note that this does not allow you to save the order of the sections, because different sections could be available for different queries.

We’re excited about this small but powerful enhancement. We hope you enjoy using the new functionality, and please email us at support@collaborativedrug.com to let us know how it works for you.

We’re happy to announce the release of the latest version of CDD’s software, now available live at www.collaborativedrug.com. The big update in this release is the ability to archive information on scientific references (references as in the references section of a publication). There are two goals for this functionality: 1) to allow researchers to share lists of relevant articles with each other, and 2) to provide a convenient way to link back to the original article when curating data from literature. We have addressed the first goal with this release, and are now working on the second goal, which we plan to release soon.

With this release we’ve made it convenient to search PubMed for articles, and to then import the relevant ones into your private CDD database. You can also upload PDFs to share with colleagues in your private group (and only within your private group, which is permitted fair use of these often copyrighted materials).

A few other important fixes were also included in this release:

• (+), (-) and (+-) or (+,-) or (+/-) or (+ -) are now permitted in molecule names: This was a slightly embarrassing issue of overzealous molecule name canonicalization that caused problems for some users. You can rest easy now knowing that the name (+)-epinephrine is considered different from (-)-epinephrine by the CDD database.
• Both ChemAxon Extended SMILES and standard SMILES are now provided in Excel/SD exports. When exporting to Excel/SD file and remapping and slurping structures into CDD, always remember to use the ChemAxon Extended SMILES instead of standard SMILES. Standard SMILES is also provided if needed for other applications. Extended SMILES supports some annotations that standard SMILES does not, but MOL files do. For example, R-group labels in Markush structures, or relative versus absolute stereoconfiguration.
• We now check whether batch dates are valid dates when slurping. These will show up as errors in the QC report, instead of silently causing problems after you accept the report. So, for example, “NA” as a batch date is explicitly no longer accepted.

We hope you find the new functionality useful, and as always we welcome your feedback at support@collaborativedrug.com.