Genomics Education Partnership Research Articles

Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom.

Introducing bioinformatics-focused concepts and skills in a biology classroom is difficult, especially in introductory biology classrooms. Course-based Undergraduate Research Experiences (CUREs) facilitate this process, introducing genomics and bioinformatics through authentic research experiences, but the many learning objectives needed in scientific research and communication, foundational biology concepts, and bioinformatics-focused concepts and skills can make the process challenging. Here, the pairing of specifications grading with a bioinformatics-focused CURE developed by the Genomics Education Partnership is described. The study examines how the course structure with specifications grading facilitated scaffolding of writing assignments, group work, and metacognitive activities; and describes the synergies between CUREs and specifications grading. CUREs require mastery of related concepts and skills for working through the research process, utilize common research practices of revision and iteration, and encourage a growth mindset to learning-all of which are heavily incentivized in assessment practices focused on specifications grading.

Gene model for the ortholog of Pten in Drosophila miranda.

Gene model for the ortholog of Phosphatase and tensin homolog ( Pten ) in the D. miranda Apr. 2013 (UC Berkeley DroMir_2.2/DmirGB2) Genome Assembly (GenBank Accession: GCA_000269505.2 ) of Drosophila miranda . This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Gene model for the ortholog of Myc in Drosophila eugracilis.

Gene model for the ortholog of Myc ( Myc ) in the D. eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of Drosophila eugracilis . This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Manual annotation of Drosophila genes: a Genomics Education Partnership protocol.

Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.

Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy.

The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP's Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled Drosophila genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020-2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning environment, we provide four strategic lessons we infer toward democratizing science education. First, it appears that increasing access to scientific research and professional development opportunities by supporting virtual, cost-free attendance at national conferences attracts more faculty members to educational initiatives. Second, we observed that transitioning new member training to an online platform removed geographical barriers, reducing time and travel demands, and increased access for diverse faculty to join. Third, developing a Virtual Teaching Assistant program increased the availability of peer support, thereby improving the opportunities for student success. Finally, increasing access to web-based technology is critical for providing equitable opportunities for marginalized students to fully participate in research courses. Online CUREs have great potential for democratizing science education.

Manual annotation of Drosophila genes: a Genomics Education Partnership protocol

Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.

Classification of Features across Five CURE Networks Reveals Opportunities to Improve Course Design, Instruction, and Equity.

Course-based undergraduate research experiences (CUREs) are tools used to introduce students to authentic participation in science. Several specific CUREs have been shown to benefit students' interest and retention in the biological sciences. Nevertheless, CUREs vary greatly in terms of their context, methodology, and degree of research authenticity, so different types of CUREs may differently influence student outcomes. This programmatic diversity poses a challenge to educators who want to better understand which course components and features are reliably present in a CURE curriculum. To address these issues, we identified, catalogued, and classified 112 potential features of CUREs across the biosciences. To develop the list, we interviewed instructors experienced with teaching individual and large networked CUREs across a diversity of the biological disciplines, including: Squirrel-Net (field-based animal behavior), SEA-PHAGES (wet lab microbiology and computational microbiology), Tiny Earth (environmental and wet lab microbiology), PARE (environmental microbiology), and the Genomics Education Partnership (eukaryotic computational biology). Twenty-five interviewees contributed expert content in terms of CURE features and classification of those items into an organized list. The resulting list's categories encompasses student experiences with the following: (i) the scientific process; (ii) technical aspects of science; (iii) the professional development associated with research; and (iv) building scientific identity. The most striking insight was that CUREs vary widely in terms of which features they contain, since different CUREs will by necessity have different approaches to science and student involvement. We also identified several features commonly thought to be crucial to CUREs yet have ambiguous definitions. This ambiguity can potentially confound efforts to make CUREs research-authentic and aligned with the central goals of science. We disambiguate these terms and represent their varied meanings throughout the classification. We also provide instructor-friendly supplementary worksheets along with considerations for instructors interested in expanding their CURE course design, instruction, and equity.

The Genomics Education Partnership: First findings on genomics research in community colleges.

The Genomics Education Partnership (GEP), a consortium of diverse colleges/universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with internet access, may be particularly accessible for 2-year institutions with limited research capacity and significant budget constraints. To understand how GEP supports student research at CCs, we analyzed student knowledge and self-reported outcomes. We found that CC student gains are comparable to non-CC student gains, with improvements in attitudes toward science and thriving in science. Our early findings suggest that the GEP model of centralized support with flexible CURE implementation benefits CC students and may help mitigate barriers to implementing research at CCs.

Abstract 2138: The Genomics Education Partnership empowers faculty from a variety of institutions to successfully integrate genomics research experiences into undergraduate courses by providing flexible implementation strategies, ready-made curricula, a support network

Abstract 2138: The Genomics Education Partnership empowers faculty from a variety of institutions to successfully integrate genomics research experiences into undergraduate courses by providing flexible implementation strategies, ready-made curricula, a support network

Manual annotation of Drosophila genes: a Genomics Education Partnership protocol

Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.

Student Attitudes Contribute to the Effectiveness of a Genomics CURE.

ABSTRACTThe Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student’s epistemic beliefs to achieving positive learning outcomes.

The Genomics Education Partnership As A Model of Course‐Based Undergraduate Experience (CURE) that Promotes Growth Mindset

The Genomics Education Partnership (GEP) is a community of practice aiming to integrate genomics research into undergraduate curriculum while providing support to faculty in the process. It consists of more than 200 members in over 180 undergraduate institutions across the United States. Following training, faculty can claim annotations from one or more distinct projects (F element, Pathways, Parasitoid Wasps, Puerto Rican parrot) to integrate in their classes. Students participating in these projects annotate previously unstudied genomes, which are then used in analyses to answer specific scientific questions by the project lead faculty. Each of these projects is facilitated by curated curricula and customized online Bioinformatics tools. This approach has several advantages, including enabling faculty to scale research experiences to whole classrooms (unlike the wet lab apprentice model), the lack of safety issues, and the ease of transition to online delivery. Importantly, mistakes in annotations are not costly, and students can revisit their annotations to correct them. This makes the research amenable to peer instruction. While students may initially experience some frustration, they can consult with their faculty, their peers, and/or virtual teaching assistants to amend their errors. Thus, the GEP model allows for learning gains through a growth mindset, where abilities are developed through the research process. Faculty report that struggles are beneficial to the students, and that they are more likely to allow students to fail in a GEP research project than in wet lab/field work. Student outcomes are routinely assessed by a pre/post quiz and survey. While positive outcomes are observed overall, our current research indicates that these can be enhanced by early interventions that reinforce the nature of science and the agency of individual student researchers. The GEP always looks to grow its network of faculty and increase the diversity of the community.

Genomic Annotation of Chromosome 3L in Drosophilaananassae

The Genomics Education Partnership (GEP) is a nationwide community of more than 100 colleges and universities dedicated to facilitating undergraduate biology education and research. GEP provides training, resources, and mentorship to provide students with experiential learning and research experiences in genomics and bioinformatics. Comparative genomics is important for understanding organismal evolution, adaptation and gene conservation. Comparative genomics also advances the understanding of gene function and homology between species.Drosophila melanogaster is one of the most commonly used model organisms in biomedical science to study fundamental genetics as well as tissue and organ development. The smallest chromosome in Drosophila melanogaster is chromosome 4, also known as the Muller F element, with an estimated size of 5.2 Mb. While the F element has maintained a similar size in many other Drosophila species, it is substantially larger in at least four Drosophila species, one of which is Drosophila ananassae. The D. ananassae Muller F element is more than 18.7 Mb in size. A portion of the D. ananassae genome was annotated for comparison to Drosophila melanogaster. Annotations were completed to generate gene models for genes in Contig 26 of the D. ananassae 3L chromosome (Muller D element) as a comparison to the Muller F element in this species. This was completed using the UCSC Genome Browser, Gene Record Finder, FlyBase, the Basic Local Alignment Search Tool (BLAST) and gene prediction software, such as GENSCAN.Models for four genes were generated from this genomic region: CG8757, Hml, Tsp68C and CG3795. These genes showed a high level of conservation when comparing Drosophila ananassae and Drosophila melanogasterorthologues. The Hml gene codes for hemolectin, which has an orthologue in humans known as the vWB factor. The CG3795 gene has orthologs in multiple species, including Drosophila melanogaster and Drosophila bipectinata, and was recently reported to be involved in proteolysis and serine‐type endopeptidase activity. CG8757, which is predicted to have dehydrogenase activity in D. melanogaster, exhibited synteny with the orthologous gene on the 3L chromosome in Drosophila melanogaster. However, the order of these in D. melanogaster was determined to be different than those annotated in D. ananassae, suggesting a genome rearrangement has occurred in this region. Interestingly, homology with another gene, CG9150, was observed as well. Synteny analysis indicated this gene is located on the X‐chromosome in D. melanogaster, and further analysis suggests a genome rearrangement in this region as well. This annotation has provided some insight to potential genome rearrangements that have occurred in the evolutionary history of these species. Further analysis will provide a greater understanding of how Drosophila genomes have changed over time.

Examining Rates of Evolution Within the Drosophila Insulin Signaling Pathway

We are interested in understanding the evolutionary rates of genes that function in a biological network. We focused on the insulin signaling pathway due to its conservation across the animal kingdom, with literature documenting many interactions within this pathway. We used synteny and sequence similarity to identify orthologs of Drosophila melanogaster genes in a variety of Drosophilaspecies. Our focus included genes seen as central to the pathway such as Pdk1 and Tor as well as other genes such as HDAC4and srlwith at least one known connection to insulin signaling. In collaboration with the Genomics Education Partnership, we performed manual gene annotations to derive accurate protein coding sequences within our species of interest. We took a comparative genomics approach using BLAST and data from the UCSC Genome Browser, including RNA‐seq, additional alignment algorithms, and gene predictors to inform identification of exon‐intron boundaries. Comparison of the determined protein coding sequences from the target Drosophila species to the established sequences from D. melanogasterprovides insight into how a gene has been evolving since these two species diverged. Initial analysis suggests large variability in the rates of evolution taking place in our genes of interest and some correlation between higher expression level and greater sequence conservation. We are also considering our data with respect to a gene’s position within its network and its role in biological pathways to help illuminate which factors dictate gene evolution rate. We hope our methodology and results can add to our understanding of gene evolution across biological systems.

Conservation of the trblGene Across Drosophila Species: How Does Structure Support Function?

In collaboration with the Genomics Education Partnership (thegep.org), we seek to understand how genes functioning in the insulin signaling pathway evolve. In Drosophila melanogaster, the gene tribbles(trbl) codes for a protein that binds to Akt (also known as Protein Kinase B) and blocks Akt‐mediated insulin signaling. Trbl misexpression also affects the Akt target, Foxo (Forkhead box transcription factor). In humans, expression of trblorthologs is associated with degradation of substrates through E3 ligase‐dependent ubiquitination. Misexpression of TRIB2, one of the three Tribbles pseudokinases in humans, has been found to be associated with certain cancers. Our initial research consisted of annotating orthologs of trbland more recently foxoacross the genus Drosophilato look at conservation within the fly species. In order to identify orthologs, we considered synteny of the genomic neighborhood and determined conservation with the D. melanogasterprotein using BLAST. We then determined the location of the coding exons using data available in the UCSC Genome Browser, creating a gene model to evaluate how well our proposed gene matches the D. melanogaster ortholog. In addition to this process, we also used sequence alignments as well as structural databases to gather information about conservation of the Trbl orthologs among seven species. Trbl orthologs across Drosophilashow 60‐70% amino acid similarity. The highest degree of conservation is within the pseudokinase domain, which takes up the majority of the structure of the gene, for both Drosophilaand humans. Multiple sequence alignments reveal that the N‐ and C‐termini show less conservation and are shorter in human orthologs as compared to Drosophila proteins. This is significant as those regions in human TRIBs have documented functions in protein degradation. Continuing this work, we hope to gain a better understanding of how the structure of Trbl/TRIB proteins supports their function, including with other players in the insulin signaling pathway.

Growing and Sustaining a Nationwide Course‐based Undergraduate Research Experience (CURE): Genomics Education Partnership Enhances Research Opportunities at Diverse Institutions

The Genomics Education Partnership (GEP) is a community of practice focused on integrating genomics research experiences into undergraduate curriculum and supporting faculty in this endeavor. Founded in 2006, GEP has grown to over 100 participating two-year and four-year institutions and introduced thousands of students to eukaryotic gene structure, comparative genomics, and genome evolution. GEP members contribute their expertise and enthusiasm to the community through four committees: science and IT, curriculum development, assessment, and professional development and mentoring. Digital communication tools facilitate collaboration in this geographically distributed community while regional nodes enable the development of local initiatives. Our education research is focused on student experiences, attitudes, and learning gains in the CURE setting. An important dimension of CUREs that distinguishes them from the traditional laboratory classroom is iteration: students have opportunities to make mistakes and re-do (Auchincloss et al, 2014). The scaling of undergraduate research from an apprentice model to the classroom, however, poses a major challenge for faculty, creating the need to provide feedback to a large number of inexperienced student researchers. We find that custom bioinformatics tools provide rapid feedback to GEP students and allow for iterative revisions of student projects. Student surveys and focus groups reveal that bioinformatics CUREs foster “formative frustration,” whereby students can safely fail in their original analysis, adjust, recover, and succeed; students value this experience. During the COVID pandemic, GEP has provided an authentic research experience that can be delivered remotely. Bioinformatics resources are available online, as are GEP virtual tutors. Thus, GEP is a viable option for undergraduate research projects even for online learning. We are expanding our repertoire of scientific projects. GEP has partnered with Galaxy to develop G-OnRamp, an open-source platform for constructing UCSC Assembly Hubs and JBrowse/Apollo genome browsers to facilitate collaborative annotation of eukaryotic genomes. These tools allow us to include investigations of the evolution of venom in parasitoid wasps and an investigation of the evolution of genes in Drosophila biochemical pathways. We seek to grow our network of faculty and to increase the diversity of our community by making a variety of training opportunities available, including online mentoring via the QUBES platform and regional node workshops. We have created a supportive community of faculty and welcome new colleagues (no experience necessary!) eager for the challenge of bringing genomics research to undergraduate students at all levels. Faculty interested in joining the GEP can contact us at http://gep.wustl.edu/contact_us.

Annotation Parasitoid Wasp Venom Transcripts

Parasitoid wasps infect other arthropod species to complete their life cycle by laying their eggs on the surface or body cavity of their host. Many species inject a venom that alters host physiology to allow eggs to complete their development. The venom contains toxins that can disrupt host immune cell signaling, metabolism, and gene regulation. Recent venom studies used an approach that combines transcriptome or genome sequencing with the purification of venom proteins and mass spectrometry to identify venom proteins. In the Genomics Education Partnership (GEP), we are annotating parasitoid wasp genes from three parasitoid species that infect fruit flies (Drosophila melanogaster). Here, I used the University of California Santa Cruz Genome Browser mirror that combines genome, transcriptome, and proteome data, along with sequence alignment tools, to map precise coding regions of three venom gland transcripts from Leptopilina boulardi, L. heterotoma, and Ganapsis species. Each of these transcripts aligned with the jewel wasp (Nasonia vitrepennis) ortholog for MDH2 and have a similar predicted gene structure to the Nasonia and Drosophila MDH2 orthologs. Additionally, the L. heterotoma transcript aligned to a predicted uncharacterized Nasonia gene. The C-terminus of this predicted L. heterotoma protein has some similarity to the gene Shootin1 but the N-terminus of the protein has no homology to other known proteins as determined by BLAST. These gene models will be used to further investigate venom evolution and function of venom proteins in host-pathogen interactions.

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. This requires access to good genome browsers to enable annotators to visualize and evaluate multiple lines of evidence (e.g., sequence similarity, RNA sequencing [RNA-Seq] results, gene predictions, repeats) and necessitates many volunteers to participate in the work. To address the technical barriers to creating genome browsers, the Genomics Education Partnership (GEP; https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Genome Browser Assembly Hubs and JBrowse genome browsers. G-OnRamp also converts a JBrowse instance into an Apollo instance for collaborative genome annotations in research and educational settings. The genome browsers produced can be transferred to the CyVerse Data Store for long-term access. G-OnRamp enables researchers to easily visualize their experimental results, educators to create Course-based Undergraduate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomics research. In the process, students learn about genes/genomes and about how to utilize large datasets. Development of G-OnRamp was guided by extensive user feedback. Sixty-five researchers/educators from >40 institutions participated through in-person workshops, which produced >20 genome browsers now available for research and education. Genome browsers generated for four parasitoid wasp species have been used in a CURE engaging students at 15 colleges and universities. Our assessment results in the classroom demonstrate that the genome browsers produced by G-OnRamp are effective tools for engaging undergraduates in research and in enabling their contributions to the scientific literature in genomics. Expansion of such genomics research/education partnerships will be beneficial to researchers, faculty, and students alike.

Growing and Sustaining a Nationwide CURE: Genomics Education Partnership Enhances Research Opportunities for Students and Faculty at Diverse Institutions

The Genomics Education Partnership (GEP) is a community of practice focused on the integration of genomics research experiences into undergraduate curriculum and supporting faculty in this endeavor. Founded in 2006, GEP has grown to 100+ participating institutions and introduced thousands of students to eukaryotic gene structure, comparative genomics, and genome evolution. Recently, GEP has transitioned to a collaborative leadership structure. GEP members contribute their expertise and enthusiasm to the community through four committees: science and IT, curriculum development, assessment, and professional development and mentoring. Digital communication tools facilitate collaboration in this geographically distributed community and allow faculty with similar interests to work together. We seek to grow our network of faculty and to increase the diversity of our community by making a variety of training opportunities available, including online mentoring via the QUBES platform and regional node workshops. We are also expanding our repertoire of scientific projects. GEP has partnered with Galaxy to develop G‐OnRamp, an open‐source platform for constructing UCSC Assembly Hubs and JBrowse/Apollo genome browsers to facilitate collaborative annotation of eukaryotic genomes. These tools allow us to expand GEP projects, for example, to include investigations of the evolution of venom in parasitoid wasps and an investigation of the evolution of insulin pathway genes across 27 Drosophila genomes. Our education research is focused on student experiences, attitudes, and learning gains in the Course‐based Undergraduate Research Experience (CURE) setting. An important dimension of CUREs that distinguishes them from the traditional laboratory classroom is iteration: students have opportunities to make mistakes and redo (Auchincloss et al, 2014). The scaling of undergraduate research from an apprentice model to the classroom, however, poses a major challenge for faculty, creating the need to provide feedback to a large number of inexperienced student researchers. We find that custom bioinformatics tools provide rapid feedback to GEP students and allow for iterative revisions of student projects. Student surveys and focus groups reveal that bioinformatics CUREs foster “formative frustration,” whereby students can safely fail in their original analysis, adjust, recover, and succeed; students value this experience. We have created a supportive community of faculty and welcome new colleagues (no experience necessary!) eager for the challenge of bringing genomics research to all undergraduate students (freshmen through seniors). Faculty interested in joining the GEP can contact us at http://gep.wustl.edu/contact_us.Support or Funding InformationSupported by NSF IUSE‐1915544 and NIH IPERT‐1R25GM130517‐01 to LKR.

Annotation of Contig53 on Chromosome 3L of Drosophila takahashii

DNA wraps around histones to form chromatin in the nucleus of eukaryotic cells. DNA densely packed histones, heterochromatin, is associated with silencing or transcription inactive genes. While, the loosely packed chromatin, euchromatin, is associated with actively transcribed genes. The F element, dot chromosome in Drosophila melanogaster is composed of mostly heterochromatin, yet has active transcribed genes. The goal of our research is to elucidate the regulatory motif within the dot chromosome by comparing the dot chromosome genes with gene located in the euchromatin, D element. In this study, Contig 53 in D element from Drosophila takahashii is characterized with 7 features. Through the creation of a gene model or outline of where exons and introns begin and end, instances of where regulatory motifs occurs can be observed. The Genome Browser allows for visualization of the predicted genes and isoforms. BLAST allows for the alignment of genes between the two species. FlyBase contains genetic and molecular data for Drosophila melanogaster. By annotating and comparing different contigs or gene segments of the two species and the divergence between two different species D. melanogaster and D. takahashii can be visualized as well as any silencing of genes that has occurred through evolution. Our research shows that although many of the jim isoforms vary slightly, data can be correlated with RNA seq, Gene scan predications, and TopHat predictions. Of 11 total isoforms of D. melanogaster, seven share almost 90% similarity to D. takahashii. This shows that through evolution, contig 53 of D. takahashii and D. melanogaster have only diverged marginally.Support or Funding InformationThis project was supported in part by grants from the Department of Education (Award #P031S150199), from Southern California Edison, and through Vanguard University’s SURP Program generously supported by the Office of the Provost and the Institute for Faculty Development.”Special thanks to the Genomics Education Partnership (GEP)