Drosophila yakuba – Tsc1
Lose, B; Myers, A; Fondse, S; Alberts, I; Stamm, J; Youngblom, JJ; Rele, CP; Reed, LK (2021). Drosophila yakuba – Tsc1. microPublication Biology. 10.17912/micropub.biology.000474.
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Drosophila Pathways
GEP Program Director Wins Outstanding Professor Award
We are pleased to announce that GEP’s Program Director—Dr. Laura Reed—was awarded the Outstanding Professor Award at The University of Alabama.
Read the press release for more information.
2021 Pathways GEP Summer Research Fellows
During Summer 2021, nine Summer Fellows from The University of Alabama and Oklahoma Christian University reconciled coding region annotation projects from the Pathways Project. The Summer Fellows—James O’Brien, Ryan Dufur, Aidan Long, Cole A. Kiser, Ashley Morgan, Alyssa Koehler, Annie Backlund, Jhilam Dasgupta, and Rachael Cowan—were mentored by Dr. Laura K. Reed with support from Chinmay P. Rele both of which are at The University of Alabama.
Collectively, the Summer Fellows reconciled 102 gene models. Approximately 10% of the submitted gene models were in congruence with the final gene models. The most common annotation error in the submitted gene models was improperly assigning synteny (62%). The image above illustrates the preliminary reconciliation statistics for the types of annotation errors for the Pathways Project in Summer 2021.
Reconcilers primarily focused on a single gene each, so that they could perform deeper analysis on the evolution of that gene within our selected clade. Presentations summarizing each of their work are publicly available on Box.
The Summer Fellows also generated microPublication documents. Multiple models of four genes (Tor, Ilp3, raptor, and Dsor1) will be sent to microPublication for review by the end of September 2021. Five of the reconcilers will continue to work with the Pathways Project team to reconcile gene models and send them for publication.
Collectively, the Summer Fellows reconciled 102 gene models. Approximately 10% of the submitted gene models were in congruence with the final gene models. The most common annotation error in the submitted gene models was improperly assigning synteny (62%). The image above illustrates the preliminary reconciliation statistics for the types of annotation errors for the Pathways Project in Summer 2021.
Reconcilers primarily focused on a single gene each, so that they could perform deeper analysis on the evolution of that gene within our selected clade. Presentations summarizing each of their work are publicly available on Box.
The Summer Fellows also generated microPublication documents. Multiple models of four genes (Tor, Ilp3, raptor, and Dsor1) will be sent to microPublication for review by the end of September 2021. Five of the reconcilers will continue to work with the Pathways Project team to reconcile gene models and send them for publication.
GEP’s Prototype microPublication is Published
GEP’s first/prototype microPublication has been published! Now that we have made it all the way through the process with the first one we will be moving quickly to submit the additional manuscripts that are ready to go.
Rele, CP; Williams, J; Reed, LK; Youngblom, JJ; Leung, W (2021). Drosophila grimshawi – Rheb. microPublication Biology. 10.17912/micropub.biology.000371.
Pathways Project: Annotation Videos
This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.
Pathways Project: Annotation Workflow
The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.
Pathways Project: Annotation Report Exemplar
GEP students use the Annotation Report form to submit their annotation results for the Pathways Project. The Annotation Report Exemplar is provided as an example of a completed report.
Pathways Project: Annotation Report
GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report.
Pathways Project: Annotation Notebook D. pseudoobscura Homework Key
Students can apply what they learned in the Pathways Project: Annotation Walkthrough to construct a gene model for Rheb in D. pseudoobscura by completing the Pathways Project: Annotation Notebook. An answer key is provided to assist in checking the accuracy of the annotation and includes potential areas of confusion throughout.
Pathways Project: Annotation Notebook
The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.
