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Please join us on October 15-18, 2018 at the EMBL-EBI campus in Cambridge/UK to learn how to analyze RNAseq data in zebrafish. 


In this hands-on course, participants will learn how to design functional genomics experiments and how to manage and analyse such datasets from zebrafish and to compare these to other species. The course will be relevant to researchers working on a wide range of topics, but will use a number of cancer datasets as the basis for hands-on analysis. The final day will provide participants with an opportunity to apply the tools and resources introduced during the previous teaching sessions by undertaking a short problem solving session.


Audience: This course is aimed at researchers currently working with zebrafish and generating genomic and functional data. No prior bioinformatics knowledge is required, but knowledge of R and web-based packages would be beneficial. Trainees with limited experience of R will be provided with pre-course preparation materials to increase their R knowledge.  Trainees, junior and senior group leaders are all invited to apply! 

Outcomes

At the end of the course you will be able to:

  • Design and implement RNA-Seq experiments using Zebrafish
  • Know and apply common approaches and tools used in the analysis of zebrafish expression data
  • Undertake basic data visualisation
  • Query RNA-Seq datasets for gene signatures
  • Undertake cross species comparison of gene datasets


https://www.ebi.ac.uk/training/events/2018/bioinformatics-functional-genomics-zebrafish


Space is limited to 30 participants and an application process is required. Deadline is July 27, 2018

Please forward and post. 


Organized by: 

 Elizabeth Busch-Nentwich (Cambridge U), Sarah Morgan (EMBL-EBI) and Kirsten Sadler (NYU Abu Dhabi) 



Dear zebrafish user community, 

we are proud to announce the first release of the DANIO-CODE track hub for zebrafish developmental epigenomics and transcriptomics datasets. It contains almost a 1000 tracks with 17 assay types (ChIP-seq, RNA-seq, ATC-seq, CAGE-seq etc.) from 38 stages of development. The raw data of 30 labs were annotated and reanalyzed by standardised pipelines to create the track hub, which is currently available to upload to UCSC or Ensembl genome browsers at https://danio-code.zfin.org

For information on how to access data, on fair use policy and how to upload new data to the resource, please visit the Data Coordination Centre: https://danio-code.zfin.org.

To learn more about DANIO-CODE visit https://www.birmingham.ac.uk/generic/danio-code/index.aspx.

For enquiries on technical matters contact daniocode@gmail.com.

For general enquiries contact daniocode.enquiries@gmail.com. 

Please spare some time to browse the datasets and to check you favourite gene, to reveal its expression and its true promoter, to predict its enhancers and non-coding RNAs around them and many more…The first release is a beta version, please send feedback to the emails above.

Acknowledgements:

Massive thank you to Matthias Hörtenhuber, Kadir Mukarram, Michael Dong and Carsten Daub at Karolinska Institutet as well as to Damir Baranasic and Boris Lenhard at Imperial College, who have been the main drivers behind the recently achieved DANIO-CODE milestone. 

Thanks extend to Marcus Stoiber at Berkeley and Ben Brown at Berkeley/Birmingham for their work at the early stages of data collecting/processing pipeline development. Anne Eagle, Monte Westerfield and their colleagues at ZFIN for hosting and managing the datasets and WIKI, Matthias Hörtenhuber, Julia Horsefield (Otago), Bernard Peers (Liege) and Shelley Jukes (Birmingham) for helping with management and Fiona Wardle (KCL), Boris Lenhard for their major contributions in lobbying/applying for funds and DANIO-CODE meeting organisations. Further acknowledgements goes to all the data producers (see DCC) particularly those, who submitted unpublished data: Elisabeth Busch-Nentwich (Sanger), Antonio Giraldez (Yale), Tatjana Sauka-Spengler (Oxford), Jose Louis Gomez Skarmeta (UPO Sevilla) and their colleagues. Finally, we need to acknowledge the financial support by the European Commission’s  H2020 Marie Sklodowska-Curie programme to ZENCODE-ITN and the BBSCR, UK. 

We hope this achievement will not only help in learning about the zebrafish genome, it will also motivate all of us to submit additional, published and unpublished datasets to keep this resource growing for the benefit of the user community. 

Again, huge thanks to those who did this great job and wishing you as much fun as we have had with browsing the datasets in their full glory:).  

best wishes, 

Ferenc

On behalf of DANIO-CODE and ZENCODE-ITN partners

Ferenc Mueller f.mueller@bham.ac.uk


The Chinese zebrafish research community has been rapidly growing in recent years. Since 2012, the Chinese Zebrafish Principal Investigator Meeting (CZPM) has been held in Wuhan by the China Zebrafish Resource Center (http://zfish.cn). The CZPM is a biennial meeting series for scientists who are interested in basic and applied science in zebrafish and other fish models. 

The 4th CZPM will take place from October 11th to 14th, 2018. The organizers welcome all participants who wish to take this opportunity to exchange research results, to share ideas, and to promote collaborations.

For more information, please visit the meeting website: http://pi2018.zfish.cn/

 

Yonghua Sun, Institute of Hydrobiology, Chinese Academy of Sciences

Feng Liu, Institute of Zoology, Chinese Academy of Sciences

Zhan Yin, Institute of Hydrobiology, Chinese Academy of Sciences

Anming Meng, Tsinghua University

We are happy to inform you that registration for the Nordic Zebrafish and Husbandry meeting is now open. The deadline for registration is the 8th of October 2018. You are invited to submit abstracts for either the oral or poster presentation. The participation fee is 1000 SEK and includes all coffee breaks, lunches and the dinner/social event.


Registration: https://survey.ki.se/nordic_zebrafish


For more information, please visit the meeting website:

https://ki.se/en/km/nordic-zebrafish-and-husbandry-meeting-2018

 

We look forward to seeing you in Stockholm in November 2018!


Dear Colleagues,

For a workshop, sponsored by ORIP/NIH end of July, we are seeking community feedback to discuss and assess the needs and challenges of developing defined diets and optimized feed management strategies that will support normal zebrafish development and physiology and will facilitate the analysis of phenotypes in a standardized nutritional environment. This will promote rigor and reproducibility in some zebrafish studies and enhance the use of zebrafish and other aquatic models in biomedical research.

A more detailed description of workshop purpose and objectives is below. The organizers would very much appreciate your thoughts on the issue. Please provide your feedback through this survey:

Workshop Organizing Committee (WOC) members:

Diana Baumann (Stowers Institute for Medical Research, MO)

Lilianna Solnica-Krezel (Washington University School of Medicine, MO)

John Rawls (Duke University School of Medicine, NC)

Robert Tanguay (Oregon State University, OR)

Zoltan Varga (ZIRC, University of Oregon, Eugene, OR)

Stephen A. Watts (Chair; University of Alabama at Birmingham, AL)

 

Follow this link to the Survey: 

Take the Survey

Or copy and paste the URL below into your internet browser:

https://oregon.qualtrics.com/jfe/preview/SV_3gTZ0U77pWzqTVH?Q_CHL=preview

Follow the link to opt out of future emails:
Click here to unsubscribe


Workshop: Defined Diets for Zebrafish and Other Aquatic Biomedical Research Models: Needs and Challenges
ORIP/DPCPSI/OD-NIH sponsored Workshop

Purpose of the Meeting: Aquatic animal species, such as zebrafish (Danio rerio), are powerful models for studying human development, behavior, genetics, and disease. The ability to produce transgenic and mutant lines provides biomedical researchers with many options for developing models of human diseases and for developing relevant therapeutic approaches. Different facilities and laboratories use a variety of diets and feeding protocols to maintain these models. In many laboratories zebrafish are reared with a combination of live feed (ex vivo) and/or one of many undefined commercial diets. Commercial diets used in zebrafish husbandry differ significantly in ingredient and nutrient composition and often contain preservatives, lakes, dyes, antinutritional factors, or bioactive food compounds. Studies indicate that the length, weight, sexual maturation, fecundity, and mortality of zebrafish can vary significantly with different diets. Unfortunately, impacts of diet on zebrafish health and behavior and corresponding implications for zebrafish research outcomes are not well described. Currently, the daily dietary nutrient requirements of almost all nutrients have not been investigated. There is also no consensus among aquatic facilities, researchers, and commercial vendors on nutritional requirements at various life stages (i.e., larval, juvenile, and adult) or for particular research applications to minimize husbandry variations among aquatic facilities or laboratories. Complicit in this lack of consensus is a community-wide lack of understanding of the role of nutrition in animal development, health, and research outcomes. To address this gap, the Office of Research Infrastructure Programs (ORIP) is sponsoring a workshop to bring together members of the zebrafish scientific community, with expertise in zebrafish and other aquatic and relevant models, for a day of discussion. The workshop attendees will assess the needs and challenges of developing defined diets and optimized feed management strategies that will support normal zebrafish development and physiology and will facilitate the analysis of phenotypes in a standardized nutritional environment. Standardization and education will promote rigor and reproducibility in some zebrafish studies and enhance the use of zebrafish and other aquatic models in biomedical research. 
 
Objectives:

  1. Review diet development strategies, where available, in other biomedical model species.
  2. Assess the current nutrition status of zebrafish.
  3. Describe the need for defined diets for maintenance and experimental stocks, including assessment of life stage requirements.
  4. Discuss the potential impact of defined diets on genetic stocks used in biomedical research, their effect on development, physiology and expressivity of disease/mutant phenotypes.  
  5. Identify obstacles and evaluate strategies that may lead to a successful consensus, acceptance, and implementation of defined diets among the different scientific community stakeholders.
  6. Define an educational approach to informing the community and associated partners (journals, organizations, granting agencies, etc.)
  7. Determine whether/how the approach to develop a defined diet for zebrafish could be applied to other aquatic models, and animal models in general.

http://www.eufishbiomed.kit.edu/300.php

In ophthalmology, clinician scientists may be unaware of the many possibilities provided by zebrafish models. On the other hand zebrafish researchers may be unexposed to pressing clinical research questions. The aim of the meeting is to bring researchers using the zebrafish model closer to the medical community. At the same time, the meeting shall introduce the virtues of the zebrafish model to clinical researchers. Keynote lectures will cover various aspects of zebrafish eye research. This will be complemented by presentations addressing research on human eye diseases with high clinicial relevance. In addition, short talks and poster presentations will be selected from submitted abstracts of meeting participants.



The 13th

International Zebrafish Conference

June 20-24, 2018

Madison, Wisconsin


Feeling depressed that you missed the deadline and won’t have the opportunity to join all your fishy friends and colleagues at the “big meeting” in Madison?  Well cheer up - you’ve got a second chance!! 


Late registration and abstract submission* are now open for the International Zebrafish Conference being held in Madison, Wisconsin, June 20-24, 2018. 

The meeting includes:

30+ plenary, concurrent, and poster sessions showcasing the latest zebrafish research

  • 12+ dynamic workshops highlighting cutting-edge new technologies
  • Numerous exhibitors displaying the latest equipment and tools for your research
  • Extensive opportunities to network with colleagues and suppliers
  • Lakeside BBQ picnic and closing banquet and party with live band and dancing
  • Inexpensive university housing and a conference meal plan for limited budgets

* Note that late abstracts can only be considered for poster presentations

Click HERE to register** and/or submit an abstract**

**In order to register for the conference and/or submit an abstract, you must sign in or create a new IZFS website profile. During profile creation you will also be given the opportunity to become an IZFS member, giving you access to discounted IZFS member conference registration rates. If you have trouble creating a profile, contact our administrator at info@izfs.org

Date: Wednesday 20th June 2018, 1-5 pm 

In association with the 13th International Zebrafish Conference, the Wellcome Sanger Institute, European Bioinformatics Institute (EBI), NCBI and ZFIN, we are pleased to announce an 'Exploring Zebrafish Genome Data' Hands-on Workshop.

This workshop covers 
• Understanding genome assemblies
• Using Ensembl to explore zebrafish data
• NCBI zebrafish resources
• ZFIN Resources

via presentations and hands-on exercises.

For more details, please go to http://www.sanger.ac.uk/generic-detail/open-door-workshop-13th-international-zebrafish-conference-20th-june-2018 or email us at zebrafish-workshop@sanger.ac.uk

When registering for the conference, you will find an option to also register for the workshop. Any problems, please let us know.

Looking forward to meeting you there!

Kerstin and Jane (workshop organisers)

Dear Zebrafish Community Members:

 

Nominations are open for the 2018 election for new members of the Board of Directors of the International Zebrafish Society (IZFS). The Board acts on the behalf of IZFS to guide the activities and direction of the Society. This is an excellent opportunity to get involved!

Zebrafish community members are invited to submit nominations by Sunday, April 15, 2018 for the following positions on the IZFS Board of Directors, for terms beginning July 1, 2018.

  • President-Elect
  • Secretary
  • Asia/Pacific Regional Director (1 vacancy)
  • Europe/Mediterranean Regional Director (2 vacancies)
  • United States/Canada Regional Director (2 vacancies)

 

https://izfs.site-ym.com/page/IZFSNominations

 

Nominees must be IZFS members in good standing who have paid their 2018 dues. We welcome nominations of individuals who are forward thinkers, strategic planners, and dedicated volunteers active in the zebrafish community. Self-nominations are welcome. 

Nominations will be reviewed by the IZFS Nominations Committee who will determine the final ballot in accordance with IZFS bylaws. Thank you in advance for your nominations.

 

Sincerely,

Sharon Amacher

Peter Currie

Mary Halloran

Mary Mullins

Stephan Neuhauss

IZFS Nominations Committee

Dear Zebrafish Research Community,


ZFIN would like your input to help prioritize updates to ZFIN web pages and services.  Please take a few minutes to respond to the 2018 Zebrafish Community Survey. 

 

https://oregon.qualtrics.com/jfe/form/SV_cVkvsFMQLqlilgN

 

Responses will help us focus effort on the most important web pages and data types and keep ZFIN as useful as possible to the research community.

 

Thanks!

The ZFIN Team

The deadline to apply for the Marine Biological Laboratory "Zebrafish Development and Genetics” summer course (August 4-18, 2017) is MONDAY, APRIL 16th.


This intensive two-week course caters to advanced graduate students, postdoctoral fellows, and independent investigators who are incorporating the zebrafish model into their research and/or teaching. Applications from underrepresented minorities are especially encouraged. 


The course covers time-proven and emerging technologies geared towards application in zebrafish. Mornings and afternoons are devoted mainly to laboratory experiments and evenings to lectures and discussions. The course is taught and guided by 20 international leaders in the field and enrollment is limited to 22 students. 


More information and application instructions are available on the following webpage:

http://www.mbl.edu/education/special-topics-courses/zebrafish-development-and-genetics/

Scholarships and financial assistance are available. 


Deadline for application: 16 April 2018


 International Zebrafish Conference (IZFC), June 20-24, 2018, Madison, WI

- 30+plenary, concurrent, and poster sessions showcasing the latest zebrafish research

- 12+ dynamic workshops highlighting cutting-edge new technologies

- Numerous exhibitors displaying the latest equipment and tools for your research

- Extensive opportunities to network with colleagues and suppliers

- Lakeside BBQ picnic and closing banquet and party with live band and dancing

- Inexpensive university housing and a conference meal plan for limited budgets

Conference Information       Registration*      Abstract Submission*

CLICK HERE

* Note: In order to register for the conference and/or submit an abstract, you must sign in or create a new IZFS website profile. During profile creation you will also be given the opportunity to become an IZFS member, giving you access to discounted IZFS member conference registration rates. If you have trouble creating a profile, contact our administrator at mailto:info@izfs.org

Letter of invitation required?  REGISTER soon as possible and request a letter of invitation on the registration form.

Travel Awards Limited funds are available for presenting member trainees or junior faculty who would otherwise be unable to attend the meeting, including specific scholarship funds for underrepresented minorities. Click HERE to apply.

Want to exhibit at or sponsor this conference? Make sure that your company or organization doesn’t miss out on the chance to be noticed at the largest and most important conference for zebrafish investigators. A variety of attractive sponsorship options are available to fit every budget. Visit the conference website “exhibit and sponsor” tab for more information or contact IZFS meeting planner Marcy Green.