Workshops and Meetings

Next Workshop: April 6-11, 2023

Course principles: BioInformatics Workshop for Xenopus Researchers:

Attendees will be wet lab researchers who want to extend their understanding of computational analysis tools and methods, and may also want to acquire grounded computational skills to enable them to work independently. They may be PIs, post docs or PhD students, but are less likely to be research technicians.

The course will involve analyzing real data to illustrate all of the skills, techniques and approaches covered. All of this data will be drawn from experimental work in Xenopus.

‘No biologist left behind!’ Skills will be taught soundly and progressively with sufficient practice, so that no reasonably competent and attentive person has trouble keeping up with the basic skills being taught.

The best kit for delivering the course’s maximum impact and take-out value will be the users own laptop.

Attendees will be encouraged to bring/develop their own mini-projects during the course, but there will be relevant data available for people who do not bring their own.

Our goal is to present a comprehensive overview of bioinformatics but will try in advance to determine which methods are likely to be of most interest to our audience.

There will be a relatively low emphasis on touring ‘useful web sites’. External data sources will be explained and referenced as they are needed.

Instructors:

Taejoon Kwon, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
Leonid Peshkin, Harvard Medical School

Workshop Costs:

Event housing, meals and registration, Single room – $1577
Event housing, meals and registration, Double (shared room) – $1207
Event meals and registration (no housing) – $650
ID Only (no housing or meals) - $300

Schedule:
Please click here to view 2023 BioInformatics Workshop Schedule.

Registration:
Please click here to register for the 2023 BioInformatics Workshop.

For additional information, please contact:

Marko Horb, Ph.D.
Director, National Xenopus Resource (NXR)
Associate Scientist, Bell Center for Regenerative Biology and Tissue Engineering
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543
Email: mhorb@mbl.edu
Office: (508) 289-7627
Lab: (508) 289-7370

Feedback from the Community

“One of our post-docs attended the 2013 Bioinformatics workshop, and the training in RNA-seq analysis and general bioinformatics approaches he learned have been crucial for our research on Xenopus tropicalis embryo development. We are now pursuing several high-throughput sequencing projects–including RNA-seq and ChIP-seq–in early Xenopus embryos, and the design of these experiments and analysis of sequencing reads would not have been possible without the specialized knowledge he gained from the Bioinformatics workshop.”

“Great! I have sent one student to the bioinformatics course and he loved the course and came back and was immediately able to help many folks in the lab with bioinformatic issues.”

“I have sent three lab members to the Bioinformatics workshop. These lab members have learned the basic skills of genomic work and now routinely perform RNA-seq and ChIP-seq analyses.”

(Previously known as PI meeting)

October 11th-14th, 2019

What is XRET?
Apart from the biennial International Xenopus conference there have been limited opportunities for Xenopus researchers to interact and discuss community events over the years. To provide greater opportunities for community discussions in alternate years, the NXR has hosted short PI meetings in 2011, 2013, 2015, and 2017. Many participants felt that the PI meetings were very valuable and we are therefore continuing these meetings at the MBL on alternate years to the International Conference. The meeting was expanded beyond just PIs and renamed Xenopus resources and Emerging Technologies Meeting

What is the goal of XRET?
The goal of the Xenopus Resources and Emerging Technologies Meeting is to provide an informal venue for discussions about new and upcoming technologies, establishing priorities for the community and allowing for more in depth discussions of individual research topics. We hope the meeting will enhance aspects relevant to the entire community and foster interactions among us. Strategic planning and advances in resources important to the community will be highlighted.

What is the format?
There will be short research talks as well as discussion groups focused on topics related to the Xenopus community. The meeting will kick off with a BBQ as in previous years.

Who should attend?
The XRET meeting is open to all Xenopus researchers, with particular emphasis on principal investigators and senior postdocs.

These meetings have become very interactive and exciting and I think this year’s meeting will be no different. I encourage all interested researchers to try and attend.

If you have any questions, please contact us at Xenopus@mbl.edu.

Next Workshop: TBD

Topics covered:

• Theoretical and practical aspects of CRISPR/Cas9 and TALENs
• Methods for genotyping (DSP, HRMA, T7E1, and others)
• Maximizing target site choice and sgRNA design
• Applications for the maternal host transfer technique combined with genome editing
• Gene targeting and homology-directed repair
• Circumventing lethal phenotypes
• Xenopus genetics and husbandry issues arising in the creation of mutant lines
• Both laevis and tropicalis will be used

The goal is for you to practice the techniques using known sgRNAs and TALENs and then use your own. Ideally, you will become competent in the techniques and implement them in your own lab. In addition for those who have limited experience in tropicalis, this is a perfect time to get comfortable with them.

Next Workshop:  TBA

Check out this article about Gary McDowell’s experience in last year’s course:
More than Just Meetings- Xenopus, Advanced Imaging Workshop

The following instructors will be returning to teach this exciting workshop once again:

• John Wallingford, University of Texas, Austin
• Lance Davidson, University of Pittsburgh
• Laura Anne Lowery, Boston College
• Jakub Sedzinski, Danish Stem Cell Institute, Copenhagen
• Scott Fraser, University of Southern California      

Topics to be covered in this imaging workshop include:

• A primer on microscopes and optics with a focus on practical considerations.
• Imaging immunostained Xenopus embryos in whole-mount.
• Live imaging of cells and tissues in intact Xenopus using fluorescent fusion proteins.
• Live imaging of cells and tissues in explants.
• Computational post-processing of images for presentation/display.
• Development of custom imaging assays for students.

Participation will be limited to 15 students. The course will be team taught by experts in Xenopus and imaging. If you have any questions, please email Xenopus@mbl.edu.