1st INCF Workshop on Needs for Training in Neuroinformatics

The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF

Developing educational iPhone, Android and Windows smartphone cross-platform apps to facilitate understanding of clinical genomics terminology

No abstract available

A cure for salmonella: Engaging students in pathogen microbiology and bioinformatics

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also conduct phenotypic detection of antimicrobial resistance and large plasmids. Isolate genomes may be sequenced by the FDA or public health laboratories (ours were sequenced by the Virginia Department of Consolidated Laboratory Services at no charge). The second half of the lesson (Module 2) involves the bioinformatic analysis of this sequence data. Students use easily accessible, primarily web-based tools such as GalaxyTrakr and Enterobase to assemble their genomes and investigate areas of interest including serotyping, identification of antibiotic resistance genes and genomic islands, and evidence of plasmids. After completion of this course, students should be able to demonstrate skills in the isolation and identification of Salmonella from natural sources, as well as skills necessary for computational analysis of microbial genomic data, particularly of members of the Enterobactericaeae. While this course consists of two modules, one focusing on laboratory skills and the other bioinformatics, either could be used as a standalone module

A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge.We have developed a bioinformatics project that provides a coursebased research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit

A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics

In their 2012 report, the President\u27s Council of Advisors on Science and Technology advocated “replacing standard science laboratory courses with discovery-based research courses”—a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates