Introduction to RADseq Analysis for Non-model Systems
WEDNESDAY, JULY 22, 2020
9:00 AM – 5:00 PM
As population genomics is being used in non-model organisms more and more, Restriction Site Associated DNA sequencing (RADseq) has become a vital tool in ecological, evolutionary, and conservation genomics. It has unlocked our ability to analyze population genetics of non-model systems in a much more cost-effective way by narrowing sequencing to a reduced, randomized subset of their genome. This allows for the identification of thousands of single nucleotide sequence differences across large numbers of individuals in populations, with the cost of full genome resequencing. However, these methods are computationally demanding and not often within the wheelhouse of many herpetologists and ichthyologists. The National Center for Genome Analysis Support (NCGAS) will run a workshop that covers an overview of RADseq analyses from receipt of sequence data through analysis of variants. NCGAS is funded by NSF to make genomic methods accessible to biologists. We do this by giving access to large computational hardware, curated sets of bioinformatics tools, and direct consultation and training.
In this course, we will cover an introduction to the data and different flavors of RADseq, clean-up of the data, mapping and filtering with and without a reference genome, and finally demo downstream applications such as phylogenetic tree construction, population structure, and primer design. Along with this, we will provide materials to make the analyses go more smoothly, such as job optimization and troubleshooting skills. The workflow will be presented as a streamlined workflow available on NCGAS's github, so that participants can return to the workflow at a later date with their own data. Demo data will be provided from published studies in herpetology, allowing for hands on practice using the workflow. This workshop is aimed at the growing number of researchers interested in the low-cost RADseq method for phylogenetic and population genetic analyses, but that may not have the specific computational background to be comfortable committing to a bioinformatically intensive methodology. By the end of the workshop, participants should have a solid concept of the overall workflow, the considerations at each step, and how to run the workflow with real sequence data. The ultimate goal being to enable more researchers to take advantage of RNAseq in non-model systems.
Sheri Sanders (National Center for Genome Analysis Support, Indiana University). Email: firstname.lastname@example.org
Specimen Collecting, Preparation, Digitization, and Usage in Natural History Collections
MONDAY, JULY 27, 2020
9:00 AM – 4:00 PM
This workshop is designed to be a hands-on learning experience on the collection and curation of natural history collection specimens. Using the VIMS Nunnally Ichthyology Collection as a laboratory, participants will learn about topics associated with specimen collection in the field, preparation, storage/curation, and usage. The target audience includes professional who are new to specimen collection and current professionals in the field.
Specimen collecting is vital for many different disciplines and learning to collect in a way that benefits both research and natural history collections is key for maximizing specimen usage. In this workshop we will discuss necessary components for field collection (e.g., permits, IACUC protocols, field notes, field collection tags, equipment, etc.) and participants will have an opportunity to collected fishes at the VIMS Teaching Marsh and Beach. We will demonstrate the kinds of data collection and processing that can occur in the field at the time of collection including: live imaging, anesthetizing/collecting with IACUC approved methods, genetic sampling, tissue storage, and fixation. Participants will then return to the lab to process these samples and additional frozen material as fluid specimens and skeletal specimens.
This workshop will then address how best to database and store various types of specimens and specimen preparations, using the VIMS Ichthyology Collection as an example. Participants will learn how to transfer specimen data into digital databases and ways to archive digital data. We will also outline best practices in collection management and the importance of long-term care of specimens. Finally, we will discuss specimen usage. We will discuss different methods for tracking in-house specimen use and how to track specimen loans outside of the institution. Participants will pack specimens for shipment according to national and international guidelines and learn how to complete necessary shipping documents. Finally, we will discuss the usage of specimens in education and outreach activities.
We feel that this workshop will appeal to both novice collectors and museum professionals. The inclusion of collections manager and curators from various museums and collections will be a valuable resource from participants. Individual collections often have different methods for storing, digitizing, and tracking specimens. Therefore, even the most seasoned museum professional will have the opportunity to learn new techniques or methods for collection and curation of specimens.
ASIH Graduate Student Workshop: Grantsmanship: Writing, Acquiring, and Navigating Grants
FRIDAY, JULY 24, 2020
12:00 NOON – 1:30 PM
Cost: No fee (Must register for this event with your meeting registration)
Being successful in science requires applying for and receiving grants to fund research. However, grants are often competitive and only the top applications can be funded. Therefore, not only is the quality of science evaluated, but the quality of the grant application is considered. Often grants require scientists to communicate research in a clear, concise way and are reviewed by panels that may not be directly involved in the same field as the applicant. It can be difficult to effectively communicate the significance of a project, the methodology, and implementation of funding requested without using jargon and while adhering to strict guidelines. Additionally, it can be a major benefit for graduate students to acquire grants early on in their career to assist in funding and experience as they progress. Budget planning can also be challenging when requesting large amounts of money. Once grants are acquired, specific details of spending and communication with grant agencies may be required to continue to receive support.
This workshop will address scientific writing and grantsmanship, including tips on writing a successful grant proposal, how to create a budget, what happens after receiving a grant, and how to find grants to apply for. A panel of experts, consisting of scientists who have been successful at securing funding, will answer your questions surrounding the topic. This workshop is aimed to be applicable to students at any point in their career. Participants are encourage to engage the panelists with their questions and concerns about funding and grant writing. Pre-registration is required for lunch to be provided to attendees, but all are welcome to attend.