DMDD DATA TO REMAIN ACCESSIBLE TO ALL

 

 

As DMDD’s five-year Wellcome Trust grant draws to a close, the analysis of all 250 knockout mouse lines is almost complete. The remaining image and phenotype data will be added to our website over the coming weeks. We are excited to announce that we have secured additional funding from the Wellcome Trust, which we believe will allow us to maintain the website for a further two years. In the long term we are seeking to identify a suitable place to archive the data, so that it can remain accessible to all.


STAY UP TO DATE

Follow DMDD on Twitter to be notified which archive(s) the data is moved to, and also to find out about any future publications. We thank you for your support and hope you will continue to use the DMDD website in the future.

NEW PHENOTYPE DATA FOR EMBRYOS AND PLACENTAS

Today, DMDD has released many new images and phenotypes for embryos and placentas from embryonic lethal knockout mouse lines. We now hold data on 70 mutant lines that have been phenotyped in detail using the Mammalian Phenotype ontology. The resulting data is freely available to the scientific community and is a potential goldmine of information about the genetic basis of developmental disorders.

The new data is accompanied by several exciting updates to our website. These include the ability to search for phenotypes by anatomy terms and the release of additional data about gene knockouts that are lethal very early in embryonic development. Highlights of the release, including examples of interesting phenotypes, can be found below.

 

SEARCH FOR PHENOTYPES USING ANATOMY TERMS

Following a major update to our search tool, users of the DMDD database can now search for phenotypes by anatomy term. This new functionality is designed to help researchers of specific organ or tissue types to quickly identify all phenotypes that are relevant to their studies. Choose from embryo and adult anatomy terms for both humans and mice.

 

Image of the DMDD search box
New search functunality gives users the option to search for phenotypes by anatomy term.

 

FIND GENE KNOCKOUTS THAT ARE LETHAL BEFORE E9.5

Around a third of the knockout lines studied by the DMDD programme have been found to cause lethality before 9.5 days of gestation. Although it is not possible for us to image and phenotype embryos from these lines, we have added them to our database and they can be found using the ‘search’ tool.

For a full list of lines that are lethal before E9.5, visit our Early lethals page.

 

EXPLORE THE NEW EMBRYO PHENOTYPE DATA

In our latest release we’ve made phenotypes available for 7 new knockout lines. These include Cfap53, which is known to be involved in left-right asymmetric patterning in humans. In mouse embryos we identified the phenotype ‘abdominal situs ambiguus’, in which the abdominal organs have neither the usual nor the mirror-image arrangement.

We have also released data on Fut8. This gene is linked to Leukocyte Adhesion Deficiency, a syndrome with symptoms including microcephaly and abnormality of the tongue and palate. In the mouse we identified various phenotypes related to the hypoglossal nerve, which controls movements of the tongue.

Some further highlights from the phenotypes released today include spinal haemorrhage in a Fut8 knockout embryo, a perimembraneous ventricular septal defect in an Arid1b knockout embryo and abnormal lens epithelium morphology in an Actn4 knockout embryo.

 

Click to view larger image.
A Fut8 knockout embryo found to have a spinal haemorrhage.

 

Click to view larger image.
Abnormal lens epithelium morphology in an Actn4 embryo. Lens epithelial cells are the parental cells responsible for growth and development of the lens.

 

 

In total, 162 distinct phenotypes were identified across 91 new mutant and wild-type control embryos. Phenotype data for a total of 81 new placentas has also been released.

 

A FULL LIST OF THE NEW DATA

HREM embryo image stacks added for Dennd4c, Dnajc8 and Pigf.

Embryo phenotypes added for Actn4, Arid1b, Cfap53, Cyp11a1, Dmxl2, Fut8 and Mfsd7c.

Placenta images and phenotypes added for B9d2, Cbx6, Commd10, Coq4, Dcx, Dhx35, Fam160a1, Gpatch1, Mfsd7c, Oaz1 and Smg1.

 

All image and phenotype data from the DMDD programme can be accessed at dmdd.org.uk. For assistance, please email contact@dmdd.org.uk.

DMDD WEBSITE ENHANCEMENTS

Following user testing of the DMDD website at the BSCB/BSDB meeting earlier this year, we’ve been working behind the scenes on some enhancements to our site. The changes went live today, and here’s a rundown of what’s new.


HOMEPAGE

Perhaps the first thing you might notice is our updated homepage. If you’re planning to search the database for genes or phenotypes, a featured ‘SEARCH’ form on the homepage will make this quicker and easier.

 

Click to view larger image.
The enhanced DMDD homepage has a dedicated ‘SEARCH’ form, as well as additional information about the project.

We’ve introduced a ‘mega menu’ at the top of the page, so you can see more information about the different sections of the website and quickly navigate to the right place. The height of the homepage has also been decreased, so it’s easier to see all the content on laptop devices.

 

Click to view larger image.
A ‘mega menu’ provides additional information about each page to help with navigation.

 

Also on the homepage: get bite-sized bits of information about the DMDD programme from the new ‘ticker’ text, sign up to our email newsletter or refresh the page to see a variety of featured images from our dataset.


NEW CONTENT

DMDD recently released a temporal gene expression profile for wild type embryos – the first step towards providing molecular phenotypes for our embryonic lethal lines. We have now added a dedicated wild type gene expression profiling page, which provides some background information and a link to the dataset itself in Expression Atlas.

A new section titled ‘OUR RESEARCH’ includes content about the DMDD consortium, our analysis techniques and a list of our publications. Protocols for placental histology, transcriptional profiling and immunohistochemistry are now available, allowing users to repeat any results of interest, while the contribution by each of our consortium member institutions is detailed on the DMDD pipeline page.

We have added additional information about the mutant lines and how they were generated, updating the About the mutants page to include allele diagrams and information about how to request lines for future research.

Finally, a dedicated section about High Resolution Episcopic Microscopy (HREM) now provides detailed instructions for the HREM imaging technique. Over time this hub of information will grow to include videos and additional information on sample dissection for HREM imaging.

A new 'HREM methods' section is a hub on information about the HREM imaging technique.
A new ‘HREM methods’ section is a hub on information about the HREM imaging technique.

COMMUNICATIONS

Our website now has a dedicated news page highlighting data releases, additional content on the DMDD blog and other news related to the project. It’s also a place to find out where you can meet us at forthcoming events, and how to connect with us via social media.

We are also keen for you to tell others about our data. You can easily download flyers or other promotional materials about the DMDD programme from our Communications materials page.


STYLE

Finally, we’ve made some changes to the style of the site to increase its usability. The most immediately visible change is the switch from a serif font, which has small projecting features called ‘serifs’ at the end of strokes, to a sans serif font, which has no ‘serifs’ and better letter spacing to make the text more readable.

We’ve also changed the layout of each embryo page to make it immediately apparent what data is available for each embryo, without requiring multiple clicks.


YOUR FEEDBACK

Part of our user testing showed that users didn’t notice the feedback button on the right edge of pages, so we’ve moved this to the top right, where users look for it.

We’re excited to launch the enhanced version of our website and would like to know what you think. If you have any suggestions just click the ‘Feedback’ link at the top right of any page on our website, or post a comment below, to let us know your ideas. Make sure to leave your details if you’d like a response or are happy for us to contact you to find out more.

WEB TESTING AT THE BSCB/BSDB MEETING

At our BSCB/BSDB exhibitor stand, we created a little web testing station, complete with ‘booth’ – the computer and user are hidden behind our poster board in this photo. Volunteers were asked to spend 10 minutes testing our website, and in return were entered into a prize draw for a £50 Amazon voucher – won by Dr Seyed Beati, from the University of Dundee.

Our stand at the BSCB/BSDB meeting
Our stand at the BSCB/BSDB meeting

 


TESTING TOOLS

Volunteers were asked to complete some short tasks on our website, which were recorded using Silverback, a usability testing tool. Silverback not only records the user’s actions on screen, highlighting where they click. It also records a small image of the user, and although it doesn’t do eye-tracking it does allow us to see if users are looking all over the screen, or frowning or looking puzzled. Silverback does all of this unobtrusively, so that users are not distracted by their own image in a video; the only indicator that they are being recorded is the camera light. The movies generated can then be reviewed to see how easy or difficult specific tasks are for users.

This is the first time we’ve done user testing with a group of people, and although it was time-consuming, the information we gathered made it worth the effort, and made us look at the website through users’ eyes. We’ve now reviewed the movies, made notes of what we observed and categorised these observations.

 


SMALL STUFF

Many of them are small things that are relatively trivial to fix. For example, we thought our website feedback link (Usersnap) on the right of the screen would be easily spotted as nothing else is around it. But it turns out that’s not the case – it seems that because no other content is near it, no-one actually looks there! So, it will be moved to the top right of the page, where most users naturally look for help.

The website feedback link, currently on the right at the edge of the screen.
The website feedback link, currently on the right at the edge of the screen.

 


BIGGER CHALLENGES

Some of the more challenging fixes relate to the usability of the Stack Viewer, our online tool for exploring the HREM data. We made a lot of observations about how the controls are used on this page, and the problems with the current interface. One thing that we noticed was that the buttons to change orthogonal views are separate from the thumbnail images in the sidebar that show the view switching, so we’ll be bringing these together. In fact we’ll be bringing all the controls into a single ‘control panel’, rather than some on the side and some in the view pane.

Stack Viewer showing embryo thumbnails and buttons to select different orthogonal views.
Stack Viewer showing embryo thumbnails and buttons to select different orthogonal views.

 

The other parts of the website that presented challenges to users were Search and the ‘line page’, which shows all of the data for a particular gene. We have new search functionality already under development, and will now add in some additional changes to make this work better for users.

The line page is one of the busiest pages on the site, and we knew before the testing that it needed some improvements. The test results show us that we need to provide more context on the page to show users what’s what, and to make the actions that can be taken more prominent and easily understood (otherwise known as affordance).

Across the site we’ll also be adding more tooltips, to provide contextual help and information next to where the user is looking, as well as breadcrumb trails to help orient users.


THANK YOU!

We wouldn’t be able to make these improvements without your input, so we’d like to say a huge thanks to everyone who gave ten minutes of their time!


DMDD AT THE BSCB/BSDB SPRING MEETING

The BSCB/BSDB Joint Spring Meeting at the University of Warwick starts today, and the DMDD team are getting ready to meet you. Visit stand 18 during one of the conference breaks to find out how our database of embryonic-lethal mouse lines could help your research. And there are prizes to be won too…

BSCB/BSDB meeting logo

 

ORIGAMI MOUSE COMPETITION

If you’re wondering what to do with that spare half an hour between sessions, why not enter our origami mouse competition? Pick up some instructions at our stand and bring your completed mouse back to us no later than 2pm on Tuesday.

Origami mouse in pink flower paper

 

A £50 gift card is on offer for the best entry. But prepare to be challenged, as it’s no easy task!

We’ll announce the winner on Twitter before the end of the meeting. Follow us @dmdduk to find out if you’ve won.

 

HELP TEST OUR WEBSITE – AND BE ENTERED INTO A PRIZE DRAW

Dilbert cartoon strip
Image courtesy of Dilbert.com

With your help we want to make our website even easier to use. Spend five minutes testing it, and we’ll enter you into another prize draw to win a £50 gift card.

You’ll be given a few short tasks to complete on the website, and software will track and record your movements on screen. It will film you too. Later on we’ll review which areas of the screen you were looking at, and whether you looked particularly frustrated. This means we can work out which parts of the website we haven’t got quite right.

We’re looking forward to meeting you!