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The public portion of the FaceBase Annual Meeting will be held on May 1st at the Harvard New Research Building in Boston.
Click here for details and to register to attend.

News & Events

Updated 'curated' datasets (13 March 2017)

Updated data models

The FaceBase Hub has made a major upgrade of the underlying database schema for the Data Browser. What this means to users is that moving forward, our new data will provide far more details to help you discover data in new ways. Note that as a result, the URL schema of data records has changed and older bookmarks to datasets will no longer work.

Updated processing

The new data model requires more extensive curation of the data. To accelerate access of data to the community, we will provide access to minimally curated data sets as soon as we can after they're submitted.

Then, after a round of careful curation, we will update the datasets on the website and change their status to 'Curated'.

Newly curated datasets

Our first set of finely curated datasets are the ones we released last month.

2017 FaceBase Annual Meeting in Boston May 1-2 (03 March 2017)

The next annual meeting of the FaceBase Consortium will be held May 1-2 in Boston, MA. We are pleased to announce that once again, the first day of the meeting -- Monday, May 1st -- will be open to the general craniofacial research community and will be webcast.

During this day-long meeting, each FaceBase project will introduce themselves and describe their progress during the past year for FaceBase 2.

You can view the event page with details including how to register to attend the public portion here: 2017 FaceBase Annual Meeting.

(If you are a member of the FaceBase consortium, please contact help@facebase.org if you need help with internal registration/information.)

To attend the public portion of the meeting, please click this link to register.

Almost 30 New Datasets Released (02 February 2017)

We're kicking off 2017 with some more new datasets from FaceBase 2 projects as well as integration of gene summary information within datasets.

New Datasets

We are pleased to offer 27 new datasets from FaceBase2 projects providing new microCT images and genomic data:

New Gene Summary integration

Where available, we have integrated gene summary information with the Data Browser. You can see our currently available summaries here. On details pages for a dataset where there is a gene summary available, a "Gene Summary" field appears with a link to the information.

Updated website navigation

We have tweaked the website navigation so that the first item, "Data Browser", now offers the same search links displayed on the homepage, as well as links to the Gene Summary records available and a list of the new and pending datasets that have been or will soon be released. Links that used to be under "Data" but that were not part of the Data Browser have been moved under "Resources".

If you have any questions or issues, please email help@facebase.org.

New OCDM Version 1.7.0 Just Released (30 January 2017)

We are happy to announce the latest release of the OCDM, version 1.7.0. Click to download the archive file:

http://sig.biostr.washington.edu/share/downloads/ocdm/release/latest/ocdm.zip

The work for this release focused on homology mappings between human and mouse developmental and postnatal anatomical entities in Craniofacial Human Mouse Mouse Ontology (CHMMO). Mappings include developmental entities, from the zygote to perinatal structures at progressive stages of development, with emphasis on embryonic precursors of components of musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints).

Provisional mappings were initially carried out based on similar or same names and then verified by our domain expert. We likewise consulted the literature for homology evidence, either based on direct molecular studies or inferred vertebrate Bauplan. Bi-directional one to one and uni-directional one to null mappings at the gross anatomical level were recorded in this work.

Sign up for a FaceBase account with existing credentials (19 October 2016)

The FaceBase Hub is implementing the final update to the authentication system for the FaceBase Data Browser to give new users the option to sign up for a FaceBase account using an existing ID (i.e., campus, NIH or Google logins) instead of needing to create yet another new account.

Note that our account management system is based on Globus Auth. These changes will allow us to take advantage of more options that Globus provides for logging in to FaceBase.

On Wednesday, October 19th, we will deploy an update to the account management software. As a result, when signing up for a FaceBase account, new users will be able to select one of the many supported identity providers (from InCommon and Google). This will create an account request which will be forwarded to the FaceBase Hub for approval.

All current users will still be able to use your existing FaceBase account using the "GlobusID" option. You may also link your current GlobusID to another trusted ID.

If you have any questions or issues, please email help@facebase.org.

Website updates - New datasets and homepage (17 October 2016)

We have just published a major update to the FaceBase website - here's an overview of what you will find.

New Data

We are pleased to offer the following new datasets from FaceBase2 projects:

  • New zebrafish microCT images from the Anatomical atlas and transgenic toolkit for late skull formation in zebrafish project.

    Presented are developmental series of two different and commonly used strains for genetic analysis in zebrafish (AB and WIK). To facilitate skeletal imaging, the same samples were scanned using newly refined technique to provide selective contrast of forming skeletal elements by whole mount staining with silver nitrate (Charles et al, in review). Complementing these data, adult stages of zebrafish mutants are provided to allow broad analysis of gene function and formation of the adult skeletal form of the zebrafish skull. Mutants with identified mutations are provided.

  • Mouse images from the Epigenetic landscapes and regulatory divergence of human craniofacial traits project.

    The data are selected images showing human and chimp gene enhancers on a mouse background. The images are of whole mount and histological samples showing the expression levels of enhancer activity as revealed by LacZ staining (blue) in the craniofacial region and other structures.

New homepage and Resources Hub

We've been listening to feedback and iterating on a new "face" for FaceBase. We've streamlined the information - making it cleaner and more focused on our important offerings.

The Craniofacial Resources Hub shows all of the information available from FaceBase and our collaborators. We'll be keeping this page updated with the latest offerings. Check it out here: Resources Hub

Updated Mouse Anatomy and Skull Fly-through

Yang Chai's lab at USC has updated the Mouse Anatomy page with color-coded drawings representing cell lineages through age stages E10.5 through P0 of a C57BL/6 mouse embryo.

We have also posted a link to their 3D Mouse Skull Flythrough video that takes you on a journey through all parts of a mouse skull.

Updated authentication system

We are rolling out an update to our authentication system on Oct 19th - based on Globus Auth - that will allow new (and existing) users the ability to sign up for a FaceBase account using an existing trusted login (i.e., campus, NIH, Google).

Cleaning and curation of the backend

The Hub has been making many changes under-the-hood to curate the data.

If you have any questions or issues, please email help@facebase.org.

Weinberg and his group publish PLOS Genetics paper (28 September 2016)

Dr. Seth Weinberg, who co-helmed the 3D Facial Norms Database project from the first phase of FaceBase, has co-authored a paper identifying specific gene variations for healthy human facial characteristics.

In Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology, published on Aug. 25 in PLOS Genetics, genome-wide association meta-analyses were conducted of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry. Analyses were performed on just under one million genotyped SNPs.

"Our analysis identified several genetic associations with facial features not previously described in earlier genome-wide studies. What is exciting is that many of these associations involve chromosomal regions harboring genes with known craniofacial function. Such findings can provide insights into the role genes play in the formation of the face and improve our understanding of the causal factors leading to certain craniofacial birth defects." -- Dr. Seth Weinberg.

You can find the publication at PLOS Genetics.

Presentations from the 2016 FaceBase Annual Meeting in Denver (18 May 2016)

Our thanks go out to Trevor Williams and all of the people at the CU Anschutz Medical Campus for being wonderful hosts for the FaceBase Annual Meeting on May 2nd and 3rd. Our first day was again open to the public and attended onsite by many local students while over 40 people attended via webcast. We thank you all for joining us.

For those who weren't able to make it, we've posted presentations and videos from May 2nd that have been approved for public viewing.

  • Slides from that day are available on our Presentations page here.

  • View videos of the presentations on our YouTube playlist.

The next Annual Meeting will be in Boston on April 24-25. To keep informed, please consider signing our mailing list here.

2016 FaceBase Annual Meeting in Denver May 2-3 (02 March 2016)

The next annual meeting of the FaceBase Consortium will be held May 2-3 in Denver, Colorado. We are pleased to announce that once again, the first day of the meeting -- Monday, May 2nd -- will be open to the general craniofacial research community and will be webcast.

During this day-long meeting, each FaceBase project will introduce themselves and describe their progress during the past year for FaceBase 2.

You can view the event page here: 2016 FaceBase Annual Meeting.

We will publish more information about the agenda, webcasting and registration as details are confirmed.

To stay updated, please click this link to sign up for the 2016 Annual Meeting information list.

Upgrade to FaceBase authentication - Phase 1 on Feb 13th (09 February 2016)

We are making some changes to the FaceBase account management system to give users more options to log in to FaceBase using their organizational identities (e.g., NIH logins, Google, University accounts, etc.) Note that the existing FaceBase accounts which are provided by Globus ID (www.globus.org) will continue to function as is.

What does this mean to existing users? For most users, the impact will be minimal.

  • On February 13, you will be able to access the website and browse open FaceBase data. However, for a period of 4 to 8 hours starting from 10:00 am PST, you will not be able to login to download data. Afterwards, when you login to FaceBase, you will automatically be redirected to the Globus ID provider to authenticate your existing FaceBase username and password. The screens will look a little different than what you're used to (see screenshots below).
  • After March 1, you will still be able to log in with your existing FaceBase account (i.e. Globus ID) but you will now also have the option to log in with any of the supported identity providers.

Here are the details. We will deploy these changes in two phases:

Phase 1: Transition Period (February 13 - March 1)

During the transition period, all existing FaceBase accounts will still be usable - however, they will now be referred to as “Globus IDs”.

When you log in to FaceBase you will see an option to select an identity provider which will include a reference to “FaceBase Account (Provided by Globus ID)”. That’s your regular FaceBase account, so just choose that option.

Screenshot of transitional log in screen starting February 13th.

You will then be redirected to the Globus ID provider where you will use your current FaceBase username and password.

Screenshot of Globus ID log in screen starting February 13th.

After logging in you will also see a screen confirming that you allow FaceBase access to your identity on Globus. Click Allow and your login will be complete.

Screenshot of permission screen to allow FaceBase access to your Globus ID.

Phase 2: System Upgrade (March 1)

We will update the FaceBase account management software. As a result, when logging in to FaceBase you will be able to select one of the many supported identity providers.

You will still be able to use your existing FaceBase account using the "FaceBase Account (Provided by Globus ID)" identity provider.

However, you will also have the option to link your FaceBase account to another supported identity provider (i.e., your campus or NIH login). We will provide instructions for that closer to the transition date.

Note that you could login with a different identity provider without linking to your current FaceBase account BUT if you do so, this would create a new, separate account that will need to go through the FaceBase approval. Therefore if you want to migrate to using a different identity provider, we recommend taking just a couple of extra steps to link your accounts.

And remember, you don’t actually have to do anything, you can just use your existing FaceBase2 account as usual, the only difference is that some of the screens will look a little different.

We think this will make it much easier for folks who want to log in to download FaceBase data. We appreciate your patience during this transition.

Site updates - First new FB2 datasets now available (14 December 2015)

This month marks the first publication of data from FaceBase 2 projects plus new features for the website.

New data is now available from these projects:

  • Developing 3D Craniofacial Morphometry Data and Tools to Transform Dysmorphology (co-PIs: Rich Spritz and Ophir Klein)
  • Genomic and Transgenic Resources for Craniofacial Enhancer Studies (PI: Axel Visel)
  • Integrated Research of Functional Genomics and Craniofacial Morphogenesis (PI: Yang Chai)
  • RNA Dynamics in the Developing mouse Face (co-PIs: Trevor Williams, Joan Hooper and Kenneth Jones)
  • Transcriptome Atlases of the Craniofacial Sutures (co-PIs: Ethylin Jabs, Greg Holmes and Harm van Bakel)

This month's data includes the following experiment types:

  • Hard tissue microCT images
  • Morphometric analysis
  • RNA expression (microarray)
  • RNA expression (RNA-seq)
  • Soft tissue microCT images

Click here to view all of the new datasets

The Hub is also happy to announce these two new sections of the website.

The Gene Summary content from the legacy site is back. This section allows you to view gene expression drawings of mice by gene and, where available, includes corresponding human data.

We have also added a new page called the Mouse Matrix. This page is a table of available datasets per mouse anatomical feature and age stage. Click on a cell to see a list of links to all related datasets.

The Hub wishes you and yours a safe and happy holiday season. We are looking forward to many more updates to FaceBase offerings in the coming year.

— The FaceBase Hub

Site updates - Homepage Links and Data Browser UI (13 October 2015)

The FaceBase Hub is happy to announce an updated version of the FaceBase website and data services. We are regularly incorporating user feedback on the site and continually working to improve it. Recent changes include:

  • New links from the home page directly to specific subsets of the data in order to help you find data of interest;
  • Bookmark-able links when searching and browsing that data, which you can share with colleagues or bookmark for later use;
  • This also means that when logging in, the current state of your search experience will be preserved during your session;
  • The search and browse sidebar is now open/expanded by default on the right hand side of the data browser to simplify navigation over the data;
  • Datasets are now annotated with an additional field to identify the Experiment Type of the study;
  • And a variety of data cleaning and usability improvements to make the site easier to use.

This is an ongoing process and we will be rolling out further enhancements on a regular basis. We welcome your feedback at help@facebase.org.

— The FaceBase Hub

Legacy site has been deprecated (28 August 2015)

We have now shut down the original FaceBase site at legacy.facebase.org. You can now find the 3D Facial Norms and Cranio GUI pages on this site with FishFace to follow soon. If you are in urgent need of content that is no longer available, please contact us at: help AT facebase.org.

More updates coming so stay tuned!

Best,
FaceBase 2 Hub

Shutting down legacy site on 8/28 (20 August 2015)

The FaceBase Hub is planning to shut down the old FaceBase site at legacy.facebase.org on Friday, August 28th. By that point we will have also migrated the Facial Norms site and some other content.

If you have any concerns about this shutdown, please contact us at: help AT facebase.org.

We are also working on some new updates to this site for the fall including an improved search interface and enhanced 3D anatomical image viewer with support for volumes, 3D meshes, landmarks, and ontology based labeling.

Please sign up for our mailing list to stay informed about new features and datasets.

Best,
FaceBase 2 Hub

New FaceBase2 Site Goes Live (01 July 2015)

As of July 1, 2015, FaceBase is happy to announce the successful transition to our new website!

Note that your logins for the old site will not work on the new site. You must sign up for a new account.

We have focused on a clean, easily navigable design and have spent the most time on the new Data Browser - just click the Filter button and use the filters sidebar to drill down to the data you're looking for. You can filter by organism, investigator, data type, mouse age stage, mouse mutation, genotype, gene, chromosome and much more.

We are still migrating certain content from the old site - which is still available for a limited time at legacy.facebase.org - as well making further improvements to the usability of the site based on user feedback.

Please use this form to tell us what you think!

Site Feedback Form

We will soon be adding new data from the FaceBase2 spoke projects. To stay on top of new data and other important FaceBase news, please subscribe to our newsletter.

Thank you so much for everyone's contribution in making this site happen.

Best,
FaceBase 2 Hub

Public Beta period of new FaceBase2 Site (08 June 2015)

We have now opened up the beta version of the new FaceBase2 site to the public and are encouraging users far and wide to kick the tires and help us make the new Data Browser even better.

The FaceBase2 Hub is rolling out a new version of the FaceBase site that is scheduled to replace the current site on Wednesday, July 1st. Note that logins for www.facebase.org will not work on the new site and you will need to sign up for a new account.

Please start using the new Data Browser. We ask that you do two things:

Note that we will be continuing to update the beta site as we receive feedback and keep porting information from the old site to the new site.

Stay tuned for more information!

Beta Site Feedback Form

Thank you, FaceBase 2 Hub Coordinating Center

We welcome your feedback (07 January 2015)

This is a preview version of the future FaceBase 2 site. We would appreciate your using the following form to send us any feedback you have on making this site more usable.

Beta Site Feedback Form

Thank you, FaceBase 2 Hub Coordinating Center

2015 FaceBase Annual meeting in Marina del Rey, CA (11 December 2014)

The next annual meeting of the FaceBase Consortium will be held January 8-9 in Marina del Rey, California. We are pleased to announce that this year, the first day of the meeting -- Thursday, January 8th -- will be open to the general craniofacial research community.

During this day-long meeting, each FaceBase project will introduce themselves and describe the research goals they will accomplish through FaceBase. The Hub Coordinating Center will also give an overview of the new FaceBase website and data browser that will be unveiled in 2015.

We are especially pleased to announce that Dr. Christine Borgman will give a presentation on "TBD" at 1:15pm.

You can find more information here: [link to event page with agenda pdf]

This meeting will be webcast, so craniofacial researchers all over the country are encouraged to join.

To attend this meeting, use the following link to register and indicate whether you will be onsite or wish to attend remotely via webcast. Further instructions will be provided via email.

Click here to register for the public portion of the FaceBase 2015 Annual Meeting

Facebase.org is moving to ISI (13 October 2014)

As part of the transition of Facebase to Information Sciences Institute (ISI) at USC, the facebase.org website is moving to ISI servers the week of October 13th. There will be more updates to the Facebase online experience in 2015 so stay tuned. We do not anticipate downtime with the move, but if you are having issues with the website, please send an email to facebase [dash] hub [AT] isi.edu.

Facebase Biorepository is still available (03 October 2014)

Although the Facebase Biorepository is now closed, samples collected as part of the FaceBase Biorepository are available to researchers interested in collaborating with the University of Iowa on projects focusing on genetics and Craniofacial conditions. To learn more about available samples and sample access please contact Nichole Nidey (nichole-nidey AT uiowa.edu) or Jeff Murray (jeff-murray AT uiowa.edu).

ASHG 2013 Webcasts Now Available (12 November 2013)

Dear Colleague,

Thank you for your participation in the largest ASHG annual meeting to date!

The 63rd Annual Meeting of the American Society of Human Genetics was held on October 22-26, 2013, in Boston, MA. This year’s meeting had a record-breaking total attendance of 8,484 participants – including scientific attendees, exhibitors, press, and speakers.

Recordings of Invited Sessions and Award Presentations (audio and slides) are now available. Please go to the ASHG web portal to access the webcasts. If you don’t already have a login ID and password, you will need to first create an account. Please note that some speakers declined to have their presentations recorded or posted online.

Highlights from ASHG 2013 include:

  • Total number of meeting attendees: 8,484
    • Scientific attendees (Members/Non-members/Speakers/Press): 6,777
    • Exhibit personnel: 1707
  • The 2013 Scientific Program featured six plenary sessions, 405 platform, and 3,469 poster presentations. There were also 21 invited sessions and 12 invited workshops programmed.
  • The 2013 Exhibit Hall was the largest ever, featuring 235 companies displaying genetics products, services, and industry publications in 327 booths.
  • Over 4,300 tweets* using the #ASHG2013 hashtag:

ASHG looks forward to seeing you next year in San Diego, October 18-22. You are encouraged to submit an Invited Session Proposal or Workshop today! Submissions will be accepted through December 6, 2013.

ASHG Meetings Management

*as of 10/28/13

Axel Visel and his group publish Science paper (30 October 2013)

Congratulations to FaceBase researchers Axel Visel, Benedikt Hallgrimsson, and  David FitzPatrick and their colleagues for publishing Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers in the latest Science.

Axel's FaceBase project is Genome-Wide Atlas of Craniofacial Transcriptional Enhancers.

View article details.

View video on Youtube.