News & Events
Registration is open for the FaceBase Community Forum on Tuesday, June 13th! (09 May 2023)
We’re excited to announce that registration is now open for the 3rd Annual FaceBase Community Forum!
This year’s Forum promises to be a unique opportunity for the craniofacial research community to come together and share knowledge. The event will be held both in-person at the HSC Conference Center at University of Southern California in Los Angeles and virtually via Zoom on Tuesday, June 13th.
The agenda includes an impressive lineup of special invited talks, a panel, learning about how FaceBase can help comply with the new NIH Data Management Sharing plans and a poster session. Whether you’re joining us in-person or remotely, you’ll have access to engaging discussions and opportunities to interact with other members of the community.
Visit our event page to learn more about the exciting happenings at this year’s FaceBase Community Forum and to register today!
Application For Data And Technology Advancement National Service Scholar Program Is Open (29 March 2023)
Here is notice of an important program from NIDCR that our users may be interested in:
The Data and Technology Advancement (DATA) National Service Scholar Program, organized by the NIH Office of Data Science Strategy (ODSS), seeks and supports experienced data and computer scientists and engineers to tackle challenging biomedical data problems with the potential for substantial public health impact. Each year, projects are selected from proposals submitted by NIH institutes for the applicants to apply for. NIDCR’s project is among the 13 that are selected this year.
Application for the Program is now open here. The due date is May 15, 2023. Please help spread the word among your networks to help NIDCR to attract strong and interested candidates.
Introducing the EnamelBase resource (13 March 2023)
FaceBase is excited to introduce EnamelBase hosted by FaceBase, a sharing site for data, tools, and resources to accelerate scientific and technical progress in studying a multi-stage process of dental enamel formation called amelogenesis.
Tools and resources are available now and coming soon at https://www.facebase.org/resources/enamelbase/, including:
- Mouse Models: 20+ mutant, conditional-ready, Cre-driver, and reporter models available at MMRRC.
- In vitro bioreactor: A 3D co-culture system for the expansion and maintenance of ameloblast-like cells
- Protocols: To support secondary use of models and generation of enamel-focused datasets
- Multiple Data Types: Morphological, biochemical, histological, biophysical, high-resolution structural images, and multi-scale omics data
Save the date for the 3rd Annual FaceBase Community Forum on Tuesday, June 13th! (14 February 2023)
Join the craniofacial research community for a day of in-person and virtual knowledge sharing at the 3nd Annual FaceBase Community Forum!
The FaceBase Hub will be hosting this year’s Forum at the at the Health Sciences Campus at University of Southern California on Tuesday, June 13th.
Check this event page, your inbox (if you’re a subscriber or member), and our Twitter account for more details as they’re confirmed!
New video available describing images and imaging resources in FaceBase (13 September 2022)
The FaceBase Hub is happy to release a new video that walks you through the rich variety of imaging data and imaging resources available in FaceBase for the craniofacial research community.
View the video below (running time 5:55):
Here is a list of specific resources referenced in the video:
Histological Image Viewer
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Dataset “Activity of human neural crest enhancer near GPR158 in E11.5 transgenic mouse embryo – Tg(hg38_chr10:25522061-25522992::LacZ).”: https://www.facebase.org/id/1-3SF2
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Annotations Editor example from Dataset “Histology and schematic overview of mouse molar root development”: https://www.facebase.org/id/1-W96W
Volumetric Image Viewer
Surface Mesh Viewer
Curated Imaging Resources
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Facial scans datasets:
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Data Access Request form: https://www.facebase.org/access/request/
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3D Facial Images - Tanzania: https://www.facebase.org/id/TX4
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3D White Light Photogrammetry Images of North American Children from Denver and San Francisco: https://www.facebase.org/id/TK0
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Developing 3D Craniofacial Morphometry Data and Tools to Transform Dysmorphology: https://www.facebase.org/id/TJ0
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Interactive Zebrafish Craniofacial Atlases: https://www.facebase.org/id/1-517M
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Anatomical Image Navigation: https://www.facebase.org/image-nav/
FaceBase Hub publication in JDR Special Issue (02 August 2022)
The Hub is pleased to announce a new paper that was just published in a special issue of the Journal of Dental Research (Data-Driven Analytics for Dental, Oral, and Craniofacial Health Care) titled “FaceBase: A Community-Driven Hub for Data-Intensive Research”. This review article summarizes the last two and a half years of FaceBase’s community-driven, self-curation model and describes the resulting varied datasets published as a result. It also describes the importance of FAIR principles for data sharing.
Schuler RE, Bugacov A, Hacia JG, et al. FaceBase: A Community-Driven Hub for Data-Intensive Research. Journal of Dental Research. August 2022. doi:10.1177/00220345221107905
Abstract:
The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research of the National Institutes of Health, was established in 2009 with the recognition that dental and craniofacial research are increasingly data-intensive disciplines. Data sharing is critical for the validation and reproducibility of results as well as to enable reuse of data. In service of these goals, data ought to be FAIR: Findable, Accessible, Interoperable, and Reusable. The FaceBase data repository and educational resources exemplify the FAIR principles and support a broad user community including researchers in craniofacial development, molecular genetics, and genomics. FaceBase demonstrates that a model in which researchers “self-curate” their data can be successful and scalable. We present the results of the first 2.5 y of FaceBase’s operations as an open community and summarize the data sets published during this period. We then describe a research highlight from work on the identification of regulatory networks and noncoding RNAs involved in cleft lip with/without cleft palate that both used and in turn contributed new findings to publicly available FaceBase resources. Collectively, FaceBase serves as a dynamic and continuously evolving resource to facilitate data-intensive research, enhance data reproducibility, and perform deep phenotyping across multiple species in dental and craniofacial research.
You can view all FaceBase publications here.
Winners of the 2022 FaceBase Poster Competition! (21 June 2022)
We had an amazing time at the 2022 FaceBase Community Forum last week with great talks and interactions. Needless to say, it was also a joy to be able to see colleagues in person for the first time in years! We’ll be posting some materials available for the public soon.
But first, we wanted to celebrate our poster finalists! The posters with the top scores were:
First Place (Tie)
- Ching-Fang Chang (Cincinnati Children’s Hospital), “Alleviation of Ciliopathic Craniofacial Anomalies by Disrupting Sufu-Gli Interaction”
- Junjun Jing (USC), “Spatiotemporal Single-cell Atlas Reveals Cell Lineage Diversification During Tooth Morphogenesis”
- Tiange Qu (UCSF), “Deconstructing Calcineurin/NFAT Signaling in Species with Distinct Midfacial Outgrowth “
Second Place (Tie)
- Brandon Chacon (UCSF), “Midface Epithelium scRNAseq Reveals Spatiotemporal Dynamics in Cleft Lip/Palate Model”
- Viviana Hermosilla Aguayo (UCSF), “Tissue-specific Roles of ESCRT Machinery Component VPS25 in Craniofacial Morphogenesis”
Third Place (Tie)
- Azeez Alade (Iowa Institute for Oral Health Research), “Shared Genetic Risk Between Cleft Subtypes in the African Population”
- Jifan Feng (USC), “TGF-β Signaling Regulates Pharyngeal Muscle Development via Mediating Cell-cell Interaction”
- Mingyi Zhang (USC), “Arid1b is Indispensable in Regulating Mesenchymal Stem Cell Homeostasis”
Congratulations to our winners and all of the poster presenters at this year’s Community Forum!
Registration is open for the FaceBase Community Forum on Tuesday, June 14th! (22 April 2022)
Registration is now open for the 2022 FaceBase Community Forum!
Click here to fill out the Registration Form
Join the craniofacial research community for a day of in-person and virtual knowledge sharing at the 2nd Annual FaceBase Community Forum!
This year, we’ll be holding the Forum in-person at the Bolger Center in Bethesda, Maryland on Tuesday, June 14th. There will be invited talks, a forum panel, poster competition and special trainee programming!
You still have the option to join remotely via Zoom for the main meeting. However, in-person attendees will have access to special demos and workshops before the main meeting and showing their posters in the poster hall.
Check out the event page for more complete information!
Save the date for the 2nd Annual FaceBase Community Forum on Tuesday, June 14th! (13 April 2022)
Join the craniofacial research community for a day of in-person and virtual knowledge sharing at the 2nd Annual FaceBase Community Forum!
This year, we’ll be holding the Forum in-person at the Bolger Center in Bethesda, Maryland on Tuesday, June 14th. There will be invited talks, a forum panel, poster competition and special trainee programming!
You still have the option to join remotely via Zoom for the main meeting. However, in-person attendees will have access to special demos and workshops before the main meeting and showing their posters in the poster hall.
Registration will open next week and will include more information on fees and logistics for in-person attendance.
Check this event page, your inbox (if you’re a subscriber or member), and our Twitter account next week for the links!
Upcoming FaceBase Bootcamp for Users & Data Contributors on April 27th (24 March 2022)
The FaceBase Hub is hosting another bootcamp which includes sessions for both users of FaceBase and those who wish to contribute data. We will also be introducing new features such as imaging data search, an updated imaging data pipeline and annotations capability.
Date and Times
Wednesday, April 27, 2022
12:00 pm to 4:30 pm EDT / 9:00 am to 1:30 pm PDT
Format
The bootcamp has two scheduled tracks - one focused for users and one for data contributors:
- 12:00 pm to 1:30 pm Eastern - Users track - The FaceBase Hub will walk through the resources available on FaceBase, best practices for using the search interface, proper citation practices and how to export data.
- 2:00 pm to 4:30 pm Eastern - Data Contributors track - Learn about contributing data and how data is curated along with a live demonstration of adding metadata and uploading data.
Zoom
Zoom details will be emailed to registrants and replay videos will be available after the event.
Details
Just click this link for details and how to register: https://www.facebase.org/training/2022-04-27/
If you have any questions, please send them to help@facebase.org.
Office Hours on Wed, March 30th (14 March 2022)
Are you interested in submitting data but have some lingering questions? Is there data you’re trying to find but aren’t sure where to start?
If you have any questions about submitting your data, requesting controlled-access human data, how to best find certain data, or any other aspect of interacting with FaceBase, please register via Zoom. Once your registration has been approved, you will receive the login information. The registration form allows you to submit your question or topic ahead of time, but if you forget, you can always send it to our contact email at help@facebase.org).
PLEASE CLICK HERE TO REGISTER VIA ZOOM
Wednesday, March 30th
Start: 1:00 pm Eastern / 10:00 am Pacific
End: 2:00 pm Eastern / 11:00 am Pacific
We look forward to talking with you!
February "Office Hours" on Wed, Feb 23rd (14 February 2022)
If you have any questions about submitting your data, requesting controlled-access human data, how to best find certain data, or any other aspect of interacting with FaceBase, please register via Zoom. Once your registration has been approved, you will receive the login information. The registration form allows you to submit your question or topic ahead of time, but if you forget, you can always send it to our contact email at help@facebase.org).
PLEASE CLICK HERE TO REGISTER VIA ZOOM
Wednesday, February 23
Start: 1:00 pm Eastern / 10:00 am Pacific
End: 2:00 pm Eastern / 11:00 am Pacific
We look forward to talking with you!
This month's "Office Hours" will be on Wed, January 26th (05 January 2022)
The FaceBase Hub wishes you all a Happy New Year!
Join us for our next Office Hours when you can join and ask members of the Hub questions: about FaceBase, about the process of contributing data to FaceBase, tips for finding particular data you are looking for, or basically any question you might have regarding the FaceBase resource.
To participate, please register via Zoom to receive the login information. You may also submit a question ahead of time when you register or anytime afterward (just send email to help@facebase.org).
PLEASE CLICK HERE TO REGISTER VIA ZOOM
Wednesday, January 26th
Start: 1:00 pm Eastern / 10:00 am Pacific
End: 2:00 pm Eastern / 11:00 am Pacific
Announcing the release of MusMorph (09 November 2021)
FaceBase is excited to announce the release of a large database of standardized mouse morphology data spanning numerous genotypes and developmental stages. This dataset, deposited by Jay Devine and Benedikt Hallgrimsson of the University of Calgary, encompasses one of the largest collections in FaceBase to date. And because the data are standardized, this allows for accurate comparisons with other datasets for analysis.
Here is the complete description from the MusMorph project page:
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in an anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide rigidly aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N=10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and metadata are stored across datasets in this project directory. The atlas files and project-wide metadata can be found in the project-wide dataset. The MusMorph scripts can be found on GitHub.
Next FaceBase Hub "Office Hours" On Wed, November 17th (02 November 2021)
Join us for our next Office Hours when you can join and ask members of the Hub questions: about FaceBase, about the process of contributing data to FaceBase, tips for finding particular data you are looking for, or basically any question you might have regarding the FaceBase resource.
To participate, please register via Zoom to receive the login information. You may also submit a question ahead of time when you register or anytime afterward (just send email to help@facebase.org).
CLICK HERE TO REGISTER VIA ZOOM
Wednesday, November 17th
Start: 12:00 pm Eastern / 9:00 am Pacific
End: 1:00 pm Eastern / 10:00 am Pacific
Introducing FaceBase Hub "Office Hours" On Wed, October 27th (06 October 2021)
Starting on Wednesday, October 27th, members of the FaceBase Hub will host “Office Hours”. This is a virtual meeting time when you can join and ask members of the Hub questions: about FaceBase, about the process of contributing data to FaceBase, tips for finding particular data you are looking for, or basically any question you might have regarding the FaceBase resource.
To participate, please register via Zoom to receive the login information. You may also submit a question ahead of time when you register or anytime afterward (just send email to help@facebase.org).
CLICK HERE TO REGISTER VIA ZOOM
Wednesday, October 27th
Start: 12:00 pm Eastern / 9:00 am Pacific
End: 1:00 pm Eastern / 10:00 am Pacific
Agenda available for FaceBase Bootcamp on September 8th (01 September 2021)
Join us for our next training that with tracks for both users of FaceBase and those who wish to contribute data. We’ll also be covering some new features related to imaging data for both users and data submitters.
Click link below to view the complete agenda:
Agenda
Date and Times
Wednesday, September 8, 2021
12:00 pm to 4:30 pm Eastern / 9:00 am to 1:30 pm Pacific
Format
The bootcamp has two scheduled tracks - one focused for users and one for data contributors:
- 12:00 pm to 1:30 pm Eastern - Users track - The FaceBase Hub will walk through the resources available on FaceBase, best practices for using the search interface, proper citation practices and how to export data.
- 2:00 pm to 4:30 pm Eastern - Data Contributors track - Learn about contributing data (including metadata and data models) and how data is curated (including updated information regarding protocols) along with a live demonstration of adding metadata and uploading data.
Zoom
Zoom details will be emailed to registrants and replay videos will be available after the event.
Details
Just click this link for details and how to register: https://www.facebase.org/training/2021-09-08/
If you have any questions, please send them to help@facebase.org.
Upcoming FaceBase Bootcamp for Users & Data Contributors on September 8th (27 July 2021)
The FaceBase Hub is hosting a new bootcamp in September which will include sessions for both users of FaceBase and those who wish to contribute data.
Date and Times
Wednesday, September 8, 2021
12:00 pm to 4:30 pm Eastern / 9:00 am to 1:30 pm Pacific
Format
The bootcamp has two scheduled tracks - one focused for users and one for data contributors:
- 12:00 pm to 1:30 pm Eastern - Users track - The FaceBase Hub will walk through the resources available on FaceBase, best practices for using the search interface, proper citation practices and how to export data.
- 2:00 pm to 4:30 pm Eastern - Data Contributors track - Learn about contributing data (including metadata and data models) and how data is curated (including updated information regarding protocols) along with a live demonstration of adding metadata and uploading data.
Zoom
Zoom details will be emailed to registrants and replay videos will be available after the event.
Details
Just click this link for details and how to register: https://www.facebase.org/training/2021-09-08/
If you have any questions, please send them to help@facebase.org.
Meeting materials from the FaceBase Community Forum (23 June 2021)
Thanks to all who attended and made this event so fun and informative!
You can find the publicly available meeting materials, including slides and webcasts, on this page:
» Guide to presentations and webcasts for the 2021 FaceBase Community Forum
Keep an eye out for an announcement soon about our next Bootcamp!
Final agenda posted for the FaceBase 2021 Community Forum - there's still time to register! (07 June 2021)
Final agenda - reminder to register
The final agenda is posted for the first annual FaceBase Community Forum! Due to the size of our poster session (19 posters from labs associated with previous phases of FaceBase and new labs!) and the addition of one new speaker (Dr. Jennifer Wagner on the bioethics of facial imaging), we extended the forum another hour:
Tuesday, June 15th
1:00 pm to 5:55 pm Eastern
This event will be an opportunity for the craniofacial research community to share their discoveries and help us find ways to work together to build a stronger community that will promote more scientific discoveries.
There’s still time to register! The forum will include:
- Updates on new and upcoming FaceBase capabilities
- Invited talks
- Panel discussion on “How can we build community around FaceBase data?” with moderator Owen White (see below)
- E-poster session - three tracks (poster guide coming soon)
» Click here for the event page and registration form!
Panel: Building FaceBase data community and enhancing its impact
At 3:55 PM Eastern, We will talk about practical methods for building community around data from people who have done just that - including things that worked, things that didn’t and metrics for measuring impact.
Our moderator for the panel, “Building FaceBase data community and enhancing its impact”, is Owen White, bioinformatician and Director of the Institute For Genome Sciences at the University of Maryland School of Medicine. He is known for his work on the bioinformatics tools GLIMMER and MUMmer. Our list of panelists includes:
- Helen M. Berman, Professor Emerita Rutgers University and former Director of the RCSB Protein Data Bank
- Christine L. Borgman, Distinguished Research Professor UCLA and Director of the UCLA Center for Knowledge Infrastructures
- J. Michael Cherry, Professor of Genetics Stanford University and PI of the ENCODE Data Coordination Center
- Melissa Haendel, Chief Research Informatics Officer at University of Colorado Anschutz Medical Campus
We hope to see you next week!
New videos that provide an introduction to FaceBase and how to contribute (19 May 2021)
The FaceBase Hub has recently published two new professionally-produced videos to help people new to FaceBase to learn more about the consortium and the process of submitting data for addition to the repository:
What is FaceBase? - An introduction to FaceBase, this video describes the mission of the Consortium and the resources it provides to the craniofacial reserach community.
Submitting your data to FaceBase - Do you have data that would be of interest to craniofacial researchers worldwide? This video is a high-level overview of how you can submit information about your data to FaceBase.
And don’t forget to register for the first annual FaceBase Community Forum - being held Tuesday June 15th on Zoom. You can learn more about the event and register here:
Click here for the event page and registration form!
Register for the FaceBase 2021 Community Forum! (29 April 2021)
We are excited to announce the first annual FaceBase Community Forum on Tuesday, June 15th via Zoom! This event will be an opportunity for the craniofacial research community to share their discoveries and help us find ways to work together to build a stronger community that will promote more scientific discoveries.
There will be invited talks, a forum panel, poster session from the community and more!
You can find the agenda here, but in general you can expect the following:
Tuesday, June 15th 1:00 pm to 5:00 pm Eastern
- Updates on new and upcoming FaceBase capabilities
- Presentations by FaceBase users
- Panel discussion on “How can we build community around FaceBase data?”
- E-poster session
Click here for the event page and registration form!
We’re very much looking forward to seeing you in June!
Yang Chai to give talk at Data Sharing and Reuse Seminar on April 9th (25 March 2021)
Dr. Yang Chai is the invited speaker for the April Data Sharing and Reuse Seminar for the NIH Office of Data Science Strategy and will be talking about FaceBase–A Data Sharing Resource to Support Dental and Craniofacial Research.
Registration is now open!
Data and time: April 9 at 12:00 pm EDT
Learn more and register: https://datascience.nih.gov/news/april-data-sharing-and-reuse-seminar-yang-chai
This seminar series is open to the public.
Chai lab help develop stem cell treatment approach for craniosynostosis (12 January 2021)
The Chai laboratory of the Center for Craniofacial Molecular Biology, USC - who have been part of FaceBase from the very beginning - headed a study published in Cell that describes a stem cell-mediated suture regeneration approach that could pave the way to improved treatments for craniosynostosis.
From USC News:
Using stem cells to regenerate parts of the skull, USC scientists partially corrected a skull deformity and reversed learning and memory deficits in young mice with craniosynostosis, a condition estimated to affect 1 in every 2,500 infants born in the United States.
“I started my career as a clinician treating kids with congenital defects, and we always wanted to do something better for these patients,” said study leader Yang Chai, a University Professor and director of the Center for Craniofacial Molecular Biology at the Herman Ostrow School of Dentistry of USC.
“This stem cell-mediated suture regeneration approach truly gives us the hope that one day we can apply this as a biological solution for this biological problem.”
You can read the full article here.
FaceBase research featured in facial genetics publication on Nature Genetics (09 December 2020)
Various FaceBase researchers have published a new paper on Nature Genetics titled “Insights into the genetic architecture of the human face”:
Abstract: The human face is complex and multipartite, and characterization of its genetic architecture remains challenging. Using a multivariate genome-wide association study meta-analysis of 8,246 European individuals, we identified 203 genome-wide-significant signals (120 also study-wide significant) associated with normal-range facial variation. Follow-up analyses indicate that the regions surrounding these signals are enriched for enhancer activity in cranial neural crest cells and craniofacial tissues, several regions harbor multiple signals with associations to different facial phenotypes, and there is evidence for potential coordinated actions of variants. In summary, our analyses provide insights into the understanding of how complex morphological traits are shaped by both individual and coordinated genetic actions.
Also see an accompanying piece that John Shaffer and Seth Weinberg, (Center for Craniofacial and Dental Genetics, University of Pittsburgh), wrote for The Conversation:
This study was funded by the NIDCR. The raw source data for the phenotypes — the 3D facial surface models in .obj format — are available through the 3D Facial Norms database at the FaceBase Consortium: https://www.facebase.org/id/VWP.
Access to these 3D facial surface models requires proper institutional ethics approval and approval from the FaceBase Data Access Committee (DAC). To gain access to this data, you must first go through the process outlined here.
Bootcamp for Users on November 18th (28 October 2020)
We have a new bootcamp coming up for our FaceBase users that will help you get the most out of finding, using and sharing data and research on the FaceBase website.
When?
November 18, 2020
2:00 PM to 4:00 PM Eastern / 11:00 AM to 1:00 PM Pacific
Where?
ZOOM (details will be emailed to registrants) with replay videos available after the event
Who is it for?
For craniofacial researchers, biologists, geneticists, clinicians, and students who are interested in accessing a wide breadth and depth of craniofacial biomedical data. Whether you’re new to facebase.org or you’ve used the site for years, you’ll learn more of what’s available, some new features, and tips and tricks for getting the most out of your experience.
What?
Here’s the general agenda:
- Site walkthrough with general look at resources available
- Searching options, tips & tricks
- Metadata/data models
- How to share and properly cite data
- How to export data
- Q&A
How?
Just click this link for details and how to register: https://www.facebase.org/bootcamp/
If you have any questions, please send them to help@facebase.org.
Join the FaceBase Workshop at SCGDB Tuesday, October 20th (07 October 2020)
Join Rob Schuler, technical project manager of the FaceBase Hub, as he conducts a workshop at the Society for Craniofacial Genetics & Developmental Biology Annual Meeting this month.
FaceBase Workshop
Tuesday, October 20th
12:30 PM Eastern
For more information, see the meeting website: https://www.scgdb.org/annual-meeting.
FaceBase Bootcamp for Data Submitters Replay Videos (12 August 2020)
Thanks to all those who participated in the Bootcamp! We had a great time with 22 attendees!
We recorded the entire session and have posted them here - separated out by agenda topics so you can go directly to the session that interests you most:
Go to: https://www.facebase.org/bootcamp/2020-07-22/
Screenshot from the hands-on tutorial segment
First FaceBase Bootcamp for Data Submitters on July 22nd (08 June 2020)
We are inviting all craniofacial researchers who are interested in submitting data to the FaceBase website to join us for the first FaceBase Bootcamp for Data Submitters.
Our original intention was to be able to provide travel funding for labs to send data submitters for first hand training. Due to the Covid-19 we weren’t able to do so this year (sign up for a FaceBase account to be notified about such opportunities in 2021!) we have decided to hold this bootcamp virtually.
When?
Wednesday July 22, 2020
9am to 2pm Pacific / Noon to 5pm Eastern
Where?
ZOOM (details will be emailed to registrants) with replay videos available after the event
What?
Two-part agenda:
- Overview submission and curation process; applying data model concepts; how to install tools,
- Hands on tutorial with sample data (sequencing and imaging), hands on exercises and Q&A for your own data.
How?
Just click this link for details and how to register: https://www.facebase.org/bootcamp/
If you have any questions, please send them to help@facebase.org.
FaceBase at the Gordon Conference (05 March 2020)
Members of the FaceBase Hub attended the 2020 “Craniofacial Morphogenesis and Tissue Regeneration” Gordon Research Conference in Lucca (Barga) Italy last week and talked to many FaceBase users who were interested in using and submitting data.
PIs, Yang Chai and Carl Kesselman, along with data project leader, Rob Schuler, attended this prestigious annual meeting typically attended by graduate students, post-docs, and young career scientists as a breeding ground for sharing information and innovative ideas in the craniofacial research domain.
Chai, Kesselman and Schuler had the opportunity to interact with many FaceBase users who were enthusiastic in learning about how to submit data to the repository, provided positive feedback and shared interesting ideas for presenting our data.
The Hub also hosted an information session that was highly attended and very interactive. You can access the presentation here.
Genome Browser Integration, Related Datasets and More New Features on FaceBase (28 January 2020)
We have updated the Data Browser by integrating the UCSC Genome Browser directly in the record pages, including a section of related datasets (providing the ability to link to related FaceBase datasets and external sources such as dbGap or GEO) and upgrading the look and feel.
UCSC Genome Browser Integration
For sequencing datasets that include track data, FaceBase updates our trackhub nightly with any newly released track data. We also integrate the GB visualization right in the dataset’s record page.
For example, the screenshot below shows the detail page for the ChIP-seq of multiple histone marks and RNA-seq from e11.5 mouse face subregions dataset. You can see the Genome Browser section below the Summary.
You can scroll down further to view the data while still on the page.
Or click “Click here to view visualization in new window” to view the track on the UCSC Genome Browser.
Related Datasets section
We can now indicated datasets that are related to each other, whether in FaceBase or another repository such as dbGAP via the “Related Datasets” section. The following example is from the detail page for Sample to subject mapping file for the 3D Facial Images-Tanzania dataset.
The following is a closeup of the entries for the Related Datasets section:
Updated User Interface for the Data Browser
As a result of extensive usability testing, we’ve made some foundational changes to the style and layout of the Data Browser as you can see in the above screenshots. These changes focused on making content in the Data Browser easier to read and to standardize layout and formatting elements. For example, the section headers on a detail page are much more prominent, more distinguishable from the rest of the content and easier to scan.
Announcing FB3 - Downloads no longer require sign-in, we're accepting data from the community! (07 November 2019)
We are happy to officially announce the third phase of FaceBase! This new phase kicked off in early fall and we are hard at work on many changes over the next five years that will make FaceBase an even more open and useful resource for the community. But for now here are the two biggest updates:
Opening up data submissions
The former hub and spoke format of the previous two versions of FaceBase is no more. We still have the Hub as the coordinating center and innovators of the data repository, but we no longer have a select group of projects (the spokes). Instead we are opening our repository to the craniofacial research community to help enhance our already rich data offerings.
If you have data that you think the community would find useful, please fill out this form to tell us about yourself and your data.
Downloads without login
We no longer require you to have a membership and be logged in to download our data (except for controlled-access human data, of course). This is a major shift designed to make it even easier and more seamless for our users to get the data you need for your research when you need it.
We do still encourage you to sign up for our newsletter - membership does have its privileges, such as keeping you updated on new features and new data and learning about the many exciting events we’ll be planning in the future.
Slides and Videos available from the 2019 Final Recap Webinar (22 May 2019)
Thank you to so many people who attended our webinar on Monday. We had about 86 attendees overall and over half of those came from outside the consortium! That indicates a lot of interest in the kind of resource FaceBase has become for craniofacial research.
We’ve posted presentations and videos from May 20th that have been approved for public viewing.
If you are interested in keeping in touch with the FaceBase Hub for any future news about FaceBase as a resource, sign up for a FaceBase account, or subscribe to our newsletter.
Final Recap Webinar on Monday, May 20th (29 April 2019)
As we close the second phase of FaceBase at the end of this month, we invite the craniofacial research community to join us for a special FaceBase 2 Recap webinar on Monday, May 20th where the FB2 projects will summarize their research and findings over the past 5 years. We will also delve into what the future of FaceBase will bring to the craniofacial research community.
If you would like to join us, please register using this form and we will send you the videoconferencing information and keep you updated on the details.
Date: Monday, May 20th
Start Time: 11:00 am Eastern / 8:00 am Pacific
End Time: 5:20 pm Eastern / 2:20 pm Pacific
You can find an agenda for the webinar here.
Photos, Slides and Videos available from the 2018 FaceBase Annual Meeting (30 May 2018)
This year’s annual meeting was another great opportunity for our spoke projects to see what everyone’s been up to and to share their work with the broader community. We now have posted the slides and videos from each of the talks on May 15th (Note that there are a couple that are not approved for sharing outside of the meeting.)
Special thanks go to Yang Chai, Linda Hattemar and the rest of the folks at the Center for Craniofacial Molecular Biology for organizing a wonderful, collaborative event for all.
We’ve posted presentations and videos from May 1st that have been approved for public viewing.
Here are some more photos from the meeting!
FaceBase Annual Meeting - Open to the Public on May 15, 2018 (09 April 2018)
The next annual meeting of the FaceBase Consortium will be held May 15-16 in Los Angeles, CA. The venue will be the Tutor Campus Center on the main campus of the University of Southern California. The first day of the meeting – Tuesday, May 15th – will be open to the general craniofacial research community and will be webcast.
During this day-long meeting, each FaceBase project will describe their project and the progress they’ve made in their particular focus on craniofacial research during the past year for FaceBase.
We are also excited to announce the Dr. Andrew McMahon, Director of the Stem Cell Institute, will be giving a talk at 3:00pm on “New Developments in GUDMAP and Possible Collaborations”.
To participate:
- Read the agenda for the public portion of meeting
- RSVP to attend Tuesday, May 15th either onsite or via webcast
(If you are a member of the FaceBase consortium, please contact help@facebase.org if you need help with internal registration/information.)
You can find more information on the event page.
UI Updates, New Datasets and Annual Meeting Dates (13 February 2018)
Read on for information about our latest data offerings, the latest UI updates to the Data Browser and dates for the next Annual Meeting.
Latest Datasets
Here are the latest data offerings from the FaceBase projects:
From Integrated research of functional genomics and craniofacial morphogenesis:
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MicroCT scans of the head tissue of Wnt1-Cre;Alk5fl/fl at P0 (FB00000911, FB00000915 and FB00000916)
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Another dataset of microCT scans of the skull of Wnt1-Cre;Alk5fl/fl at P0
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Cell Proliferation Heat Maps of:
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E 10.5 mouse embryo (two replicates: FB00000918 and FB00000919),
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From Genomic and Transgenic Resources for Craniofacial Enhancer Studies:
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4 datasets of transgenic mouse enhancer assays: mm1089, mm1094, mm1096, mm636
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ChIP-seq of multiple histone marks and RNA-seq from CS18 human embryonic face tissue
UI Updates
We’ve been taking feedback from users and submission projects and are constantly working to improve the Data Browser experience. Below are some of the recent steps we’ve taken but there’ll be many more to come in the next couple of months!
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Mouse age stages are sorted according to developmental stage (E8.5, …E10,… P0) rather than alphabetically.
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No longer displaying the dataset thumbnails.
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PubMed IDs are now displayed as either “PMID:xxxxx” or “Link to PubMed (PMID:xxxx)” depending on where they are displayed.
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Vocabulary tags (phenotype, age stage, organism, experiment type, etc.) are now displayed towards the top of the page for a dataset rather than in a new section w/ heading for each.
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Chromosome (when shown on a dataset page) is formatter per usual convention “chrN: start – end”
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We’ve stopped automatically opening a new browser tab for every new page.
FaceBase Annual Meeting 2018
We also are happy to announce the next FaceBase Annual meeting is May 15th and 16th in Los Angeles. The first day will be open to the public and you can attend either onsite or virtually. Be on the look out for the public registration form.
13 New Datasets and New Search (06 November 2017)
FaceBase has added 13 new datasets as well as introduced a new filtering interface for browsing and searching for data.
New Filtering Interface!
We are happy to announce the release of a new filtering interface that allows you to select categories within the filtering sidebar, expand or collapse them and see search results update dynamically. You can also now perform free-text searches across results.
Check out the quick video overview below (less than 2 minutes)!
New Datasets
- Two mouse datasets from Hooper/Jones/Williams: RNA Dynamics in the Developing Mouse Face:
- FB00000891 - Temporal analysis of ectoderm and mesenchyme expression in the developing mouse facial prominences with 20 samples of miRNA data.
- The second dataset is one we mentioned a couple of months ago that has since been uploaded to the FaceBase website instead of requiring download from the Mendeley website. You can access it at: https://www.facebase.org/FB00000905/
- One human (protected access) datasets from Hallgrimsson/Klein/Spritz: Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate:
- FB00000892 - 3D White Light Photogrammetry Images of North American Children from Denver and San Francisco. 750 assays of human genotype and phenotype data. This is controlled-access human data. To gain access to this data, you must first go through the process outlined here.
- Four mouse datasets from Holmes/Van Bakel/Jabs: Transcriptome Atlases of the Craniofacial Sutures: RNA-Seq data of rRNA-depleted total RNA samples extracted from laser capture microdissections of different mouse genotype and suture region at different embryonic development stages. Five biological replicate samples were profiled for each combination of mouse genotype and suture region.
- FB00000902 - Laser capture microdissections of the suture mesenchyme (SM), frontal osteogenic front (FR) and parietal osteogenic front (PA) of the coronal suture of C57BL/6J wild-type and Twist1 +/- mice at embryonic development stage TS26/E18.5.
- FB00000903 - Laser capture microdissections of the suture mesenchyme (SM), frontal osteogenic front (FR) and parietal osteogenic front (PA) of the coronal suture of C57BL/6J wild-type and Twist1 +/- mice at embryonic development stage TS24/E16.5.
- FB00000904 Laser capture microdissections of the suture mesenchyme (SM) and frontal osteogenic front (FR) of the frontal suture of C57BL/6J EIIA-Cre+;Fgfr2+/S252W (Apert) mice at embryonic development stages TS24/E16.5 and TS26/E18.5.
- FB00000906 Laser capture microdissections of the suture mesenchyme (SM) and premaxillary osteogenic front (PM) of the Interpremaxillary suture of C57BL/6J wild-type and C57BL/6J EIIA-Cre+;Fgfr2+/S252W (Apert) mice at embryonic development stages TS24/E16.5 and TS26/E18.5.
- Three mouse datasets from the Visel: Genomic and Transgenic Resources for Craniofacial Enhancer Studies project: They have generated histone ChIP-seq libraries for dissected mouse mandibular process, maxilla process and nose tissue. We performed ChIP-seq with markers of active chromatin (H3K27ac, H3K4me1) and repressive chromatin (H3K27me3). For each tissue we also generated a ChIP input library and total RNA-seq library. This is part of a series of experiments including parallel collection of dissected craniofacial tissues including maxilla, mandible and nose, and murine stages including e11.5, e13.5 and e15.5.
- FB00000909 - ChIP-seq and RNA-seq of mouse e13.5 maxillary process
- FB00000912 - ChIP-seq and RNA-seq of mouse e13.5 mandibular process
- FB00000914 - ChIP-seq and RNA-seq of mouse e13.5 nose
- Three human datasets from the Liao/Maas: Rapid Identification and Validation of Human Craniofacial Development Genes project: The purpose of this study is to collect, process, and study samples from individuals with known or possible genetic disease, and their family members. This is controlled-access human data. To gain access to this data, you must first go through the process outlined here. This trio of datasets consisted of treating the affected mother as the proband, and obtaining samples on the proband’s affected daughter and the unaffected maternal grandmother. Each dataset targets phenotypes for a different candidate gene.
- FB00000921 - FB0038_Trio Saliva_CDH1
- FB00000922 - FB0055_Trio Saliva_NFIX
- FB00000923 - FB0058_Trio Saliva_FBN2
New Gene Expression Profiles (06 September 2017)
The RNA Dynamics of the Developing Mouse Face project has published the following paper this past summer that details gene expression in the mouse facial prominences on the basis of time, prominence and tissue layer utilizing microarray platform for these analyses. They are now expanding these studies to look at isoform differences in these samples using RNAseq data that are available for download at FaceBase. The microarray data are described in this paper:
Hooper, J. E., W. Feng, H. Li, S. M. Leach, T. Phang, C. Siska, K. L. Jones, R. A. Spritz, L. E. Hunter, T. Williams. (2017). Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev. Biol. 426, 97-114. PMID: 28363736.
They are now expanding these studies to look at isoform differences using RNAseq data. They have made the processed data available as a download of HTML pages to make it easier to explore the data on a gene-by-gene basis. The relevant paper is:
Leach, S.M., W. Feng, T. Williams. (2017). Gene expression profile data for mouse facial development. Data in Brief 13, 242-247.
And the following is a link to the data itself:
https://data.mendeley.com/datasets/5y2hgyz5ng/1 (7.9 GB)
Basically, following download, an investigator can search for an individual gene and see its expression profile in the developing facial prominences as a graphical representation for time, tissue and prominence.
Here is the description from the website:
“Within this folder are three items: two folders and an index.html. Opening the top-level index.html file in a web browser will provide information concerning the two data sets. The index provides an overview, using color-coded boxes for each named gene, to illustrate the gene expression profile found within each of the data sets. Hyperlinks are also available to access details for each gene in the Whole Prominence or Ectoderm/Mesenchyme data sets.
The two subfolders, WholeProminence and EctoMesen, contain expression profiles and database annotations for every named gene available as .html pages, indexed by gene name for the two studies. Again, within each data subfolder there is a specific index for the whole prominence or ectoderm/mesenchyme dataset . There is also a folder “HTMLS” that connects directly to the list of genes and a folder “JPEGS” which has a list of images used to populate the html pages. Within the whole prominence or ectoderm/mesenchyme datasets, a gene-specific webpage visualizes the expression and detection values for each gene as heatmaps and line graphs (raw and log2 scale). Each gene-specific webpage also lists annotations from the Mammalian Phenotype, Kyoto Encyclopedia of Genes and Genomes (KEGG), InterPro and Gene Ontology (GO) databases. Terms relevant to craniofacial biology are highlighted in red.”
Take the New FaceBase User Survey! (30 August 2017)
In order to help us get a better understanding of the usefulness of this website and the craniofacial data we publish, we are asking our users to fill out a brief survey.
Almost of all of the questions are multiple choice although there are options to fill in more detail if you would like. It is also optional to include your name and we do not retain your email address (unless you agree to be contacted for further questions at the end of the survey).
This should only take a few minutes and would be invaluable information that will go towards improving this website and our contribution to the craniofacial research community.
Just follow the link below. Thank you so much for your participation!
https://uscviterbi.qualtrics.com/jfe/form/SV_9ZZHnzGBHvfyTyZ
Note, the survey will be available until Wednesday, September 16th.
New Datasets - Mouse RNA-Seq and Spry1 microCT images and landmarking protocols (09 August 2017)
FaceBase has just added a new dataset of RNA-Seq for Mouse from the RNA Dynamics of the Developing Mouse Face project: Temporal analysis of ectoderm and mesenchyme expression in the developing mouse facial prominences
We also added microCT images and landmarking protocols regarding Spry1 from the Inbred Background Genetic Effects on Craniofacial Dysmorphology project: Sprouty Background Effect. Here is the full description of this data:
Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. We use the morphometric landmarks associated with a previous FaceBase analysis (Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate) to 1) quantify the effect of three Sprouty null mutations on craniofacial shape and 2) to quantify how the associated dysmorphology is modulated by three inbred backgrounds. While it is commonly known that a given mutation may have different phenotypic effects across mouse backgrounds, our quantitative results represent an important first step towards elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice. Taking background effects into account will be necessary to identify genetic and developmental interactions that modulate the severity of craniofacial dysmorphology, because variation in the penetrance or severity of a disease mutation among humans is almost certainly based on similar interactions. In addition, identical micro-CT image and landmarking protocols make this a valuable comparative dataset to the Collaborative Cross mouse dataset of adult mouse morphology already found on FaceBase (see them listed on the Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate project page).
Presentations from the 2017 FaceBase Annual Meeting in Boston (12 May 2017)
Our thanks go out to Dr. Richard Maas, Victoria Perroni and all of the people at Harvard Medical School for being wonderful hosts for our recent Annual Meeting. Our first day was again open to the public and attended onsite as well as 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 1st that have been approved for public viewing.
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Updated FaceBase Agenda with the speaker names for each presentation (thanks for the suggestion, remote attendee Robert Cornell!)
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Slides from that day are available on our Presentations page here.
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View videos of the presentations on our YouTube playlist.
The next Annual Meeting will be in Los Angeles on May 15th and 16th. To keep informed, please consider signing our mailing list here.
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.
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Transgenic Mouse Enhancer OPT Assays - ChIP-seq, RNA-seq and transgenic assays to identify non-coding regulatory elements (enhancers) active during craniofacial development from the Genomic and Transgenic Resources for Craniofacial Enhancer Studies project.
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Alk5 Control – Bone and Soft Tissue microCT images (from E16.5 to P0) from the Integrated research of functional genomics and craniofacial morphogenesis project
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Wild Type E18.5 Frontal Suture Images from the Transcriptome Atlases of the Craniofacial Sutures project.
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:
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Transgenic Mouse Enhancer OPT Assays - ChIP-seq, RNA-seq and transgenic assays to identify non-coding regulatory elements (enhancers) active during craniofacial development from the Genomic and Transgenic Resources for Craniofacial Enhancer Studies project.
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Alk5 Control – Bone and Soft Tissue microCT images (from E16.5 to P0) from the Integrated research of functional genomics and craniofacial morphogenesis project
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Wild Type E18.5 Frontal Suture Images from the Transcriptome Atlases of the Craniofacial Sutures project.
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:
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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.
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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.
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Slides from that day are available on our Presentations page here.
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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.
You will then be redirected to the Globus ID provider where you will use your current FaceBase username and password.
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.
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!
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:
- Kick the tires a bit and contribute feedback on this form: http://goo.gl/forms/f30sfheh4H
- Sign up for your new FaceBase user account: https://accounts.facebase.org/SignIn#step=signup
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!
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.
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.