SDB Conference - Abstract Submission Guidelines:

• Save your entire abstract as a text file (.txt) to remove all formatting before starting your submission.
• The entire abstract must be one paragraph only.
• There is a 2000 character limit (with spaces) for the abstract text.
• Include any funding sources in the last sentence of your abstract.
• DO NOT copy and paste directly from your word processing program. Save your entire abstract as a text file (.txt) to remove all formatting and copy that plain text.

It costs $195 to become a full member with SDB, so we could pay $750 for one non-member to go and present a poster, or we can pay $790 for a membership+attendance and try to apply for a talk, though we don't slot well into any of the categories for the talks. Ann Loraine, which (if any) of these might we be a good fit for?

1. Developmental Bases of Diseases
2. Developmental Mechanisms for
3. Environmental Adaptation
4. Early Embryogenesis & Reproductive Biology
5. Engineering Development & Synthetic Systems
6. Epigenetic Memory and Cell Lineage
7. Evolutionary Conservation, Divergence, and Regulatory Networks
8. Metabolic Regulation and Development
9. Morphogenesis and Pattern Formation
10. Stem Cells and Regeneration

Update from scrum 4/5/24: Dr. Loraine would like us to present a poster rather than a talk. We should apply for Poster option #7 (Emerging model organisms) and present on tardigrades.

SDB

Current options are to either submit for a poster or pay to do a [workshop:https://www.sdbonline.org/uploads/files/SDB83rdAnnualMeetingProspectus.pdf].
Nowlan Freese - will email Ida Chow to determine if the cost of the workshop includes registration, or if we even need to register? If registration is included, then cost wise it would make sense to do workshop. If not, then send one person to do a poster.

Regarding SDB:

• I think we should submit a poster abstract on Wednesday and decide later on if we will also do more.

Regarding Galaxy Community Conferece:

• I think we should submit an abstract and decide later if we will go or not. The abstractr deadline is April 15. The conference itself is June 24 (around then).

I know I had said that the GCC is too expensive, but I'm reconsidering since the chance to connect with more "power users" and the Galaxy community could be worth it. However, we need to make sure that IGB still actually works well with Galaxy. i would recommend Paige Kulzer and also the rest of us look again at Galaxy and make sure IGB still works with it!

Paige Kulzer - do you have a current passport?

SDB abstract draft:

The tardigrade species Hypsibius exemplaris is an emerging model system for understanding evolution of animal development. Its small genome size, rapid generation time, transparent embryos and ease of cultivation in laboratory settings make this microscopic invertebrate amenable to experimentation using high-throughput sequencing methods such as RNA sequencing (RNA-Seq). However, advanced genomics visualization resources for Hypsibius and other tardigrade species are lacking in comparison to other invertebrates important in developmental biology. To address this lack, we developed a new genome browser resource for tardigrade using the Integrated Genome Browser, a genome browser designed for visualization of functional genomics data sets, especially RNA-Seq expression data from emerging model systems with incomplete genome assemblies. Using this new resource, researchers can perform differentially expression analysis visually, comparing publicly available RNA-Seq data sets harvested from the Sequence Read Archive.

A note for Nowlan Freese and Paige Kulzer: I can submit the abstract this evening or tomorrow. If possible, could you take a look at the abstract draft today and let me know if you have any suggestions or concerns about it?

Ann Loraine - Paige has made edits to the abstract here: https://docs.google.com/document/d/1hERYVbKeZOts4j1sJ58PUCGNihvnRdkxTkyyPjJRT00/edit?usp=sharing

Here's that final, edited version:

Presentation Title: A new genome visualization resource for exploring and visually analyzing RNA-Seq gene expression data for tardigrades (Hypsibius exemplaris and Ramazzottius varieornatus)

Abstract (one paragraph, 2000 character limit, any funding sources to be included in the last sentence):
The tardigrade species Hypsibius exemplaris is an emerging model system for understanding the evolution of animal development. Its transparent embryos, rapid generation time, ease of cultivation in laboratory settings, and small genome size make this microscopic invertebrate amenable to genome-scale assays such as RNA-Seq gene expression analysis. Other tardigrade species, including Ramazzottius varieornatus, offer models for studying resilience in the face of extreme environmental stresses, such as ionizing radiation. However, advanced genomics visualization resources for tardigrade species are lacking in comparison to other invertebrates important in developmental biology and stress resilience studies. To address this, we developed a new genome browser resource for tardigrades using the Integrated Genome Browser, an open-source genome browser well-suited for visual analysis of functional genomics data sets, especially data from scaffold (incomplete) genome assemblies like those currently available for tardigrades. This new resource contains published RNA-Seq datasets downloaded from public archives as original sequence data and then re-aligned to tardigrade genome assemblies downloaded from Genbank. The re-processed data includes sequence alignments, useful for comparing genetic differences across species, and scaled coverage graphs, useful for observing differentially expressed genes between experimental samples. In addition, researchers can use the browser to visualize their own data alongside the public, re-processed data, making it easier to interpret their work and understand its significance and impact. The Integrated Genome Browser is freely-available from bioviz.org. An award from NIH NIGMS (R35GM139609) provided funding.

Submitted abstract attached.

• Poster Theme: Emerging Research Organisms
• Do you wish to be considered for a poster teaser (One minute to present one slide about your research to entice attendees to visit your poster)?: Yes
• Short Talk Theme (1st choice): Developmental Mechanisms for Environmental Adaptation
• Short Talk Theme (2nd choice): Stem Cells and Regeneration
• Presenting Author: Nowlan Freese, nowlan.freese@gmail.com

May 9, 2024

Dear Nowlan Freese,

Thank you for submitting an abstract to present at the Society for Developmental Biology 83rd Annual Meeting. I regret to inform you that you were not selected to give a short talk this year.

Your abstract A new genome visualization resource for exploring and visually analyzing RNA-Seq gene expression data for tardigrades (Hypsibius exemplaris and Ramazzottius varieornatus) will instead be scheduled for poster presentation.

Poster session assignments will be sent out mid-June. If you have not yet registered for the annual meeting, we encourage you to do so by May 15 for the early, discounted registration rate. Visit the SDB Annual Meeting website for meeting updates.

We look forward to seeing you.

SDB 83rd Annual Meeting Program Committee

Society for Developmental Biology

6120 Executive Blvd. Suite 725

Rockville, MD 20852

301.634.7815

www.sdbonline.org