Improving the Computer Science in Bioinformatics Through Open Source Pedagogy

Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total incubation time of six months

Improving the Computer Science in Bioinformatics Through Open Source Pedagogy

Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total incubation time of six months

Standards-based Grading: An Alternative to Score-based Assessment

Standards-based grading involves assessment of student development towards achieving the course objectives throughout the duration of a course. Final course grades are then determined based on students’ overall development towards achieving the course objectives. There have been no studies to date that investigate this specific system for undergraduate science, technology, engineering and mathematics (STEM) education. This groundbreaking study involves the implementation of standards-based grading in a sophomore-level undergraduate course in Mechanics of Materials. The goals of this study are: 1) to obtain insight in how to best implement standards-based grading in an undergraduate STEM course, and 2) to obtain a sense of how students respond to standards-based grading. Students (N=30) were asked two questions at the end of the course: 1) if the standards-based grading system is more conducive to learning than the traditional, summative score-based grading system, and 2) if they prefer standards-based grading to the traditional grading system. The preliminary results suggest that the vast majority of the students, at a minimum, agree that standards-based grading is more conducive to learning (89.3%) and that they prefer standards-based grading (85.7%). Student comments also support the quantitive results. In addition, this study provides significant insight regarding implementation of standards-based grading for undergraduate courses in STEM

Standards-Based Grading: Preliminary Studies to Quantify Changes in Affective and Cognitive Student Behaviors

Assessing student learning is a key component to education. Most institutions assess learning using a score-based grading system. Such systems use multiple individual assignment scores to produce a cumulative final course grade, which may or may not represent what a student has learned. Standards-based grading offers an alternative that addresses the need to directly assess how well students are developing toward meeting the course objectives. The course objectives are the focal point of the grading system, allowing the instructor to assess students on clearly defined objectives throughout the course. The system assesses how well students become proficient in the course objectives over the duration of the course. This study extends the use of standards-based grading at the K-12 level into the realm of undergraduate science, technology, engineering, and mathematics (STEM) education. Five STEM courses pilot tested the integration of a standards-based grading system to investigate how it impacts affective and cognitive student behaviors. The results suggest that a standards-based grading system increased student domain-specific self-efficacy, was perceived as valuable, and helped students develop more sophisticated beliefs about STEM knowledge

3D Virtual Worlds and the Metaverse: Current Status and Future Possibilities

Moving from a set of independent virtual worlds to an integrated network of 3D virtual worlds or Metaverse rests on progress in four areas: immersive realism, ubiquity of access and identity, interoperability, and scalability. For each area, the current status and needed developments in order to achieve a functional Metaverse are described. Factors that support the formation of a viable Metaverse, such as institutional and popular interest and ongoing improvements in hardware performance, and factors that constrain the achievement of this goal, including limits in computational methods and unrealized collaboration among virtual world stakeholders and developers, are also considered

Breaking Boundaries in Computing in Undergraduate Courses

An important question in undergraduate curricula is that of incorporating computing into STEM courses for majors and non-majors alike. What does it mean to teach “computing” in this context? What are some of the benefits and challenges for students and instructors in such courses? This paper contributes to this important dialog by describing three undergraduate courses that have been developed and taught at Harvey Mudd College and Loyola Marymount University. Each case study describes the course objectives, implementation challenges, and assessments

The Next Step

In traditional radiology practice, reports are typically dictated and then transcribed.? While the free-text reports represent the semantic knowledge interpreted and conveyed by a physician, the information can be hard to access. The advantages of representing medical data in a structured format using standard terminology are clearly recognized. These include the ability to implement a standardized electronic medical record, automatically invoke medical guidelines when appropriate, and conduct outcomes research. Standard structured reports facilitate intelligent indexing, searching, and retrieval of documents from clinical databases. Recent attempts have been made in the industry to enable structured data entry using preformatted templates, but these have yet to gain widespread acceptance.1,2 These preformatted templates do not necessarily use standard nomenclature and tend to disturb a clinician’s normal workflow. This paper presents a prototype system that incorporates the benefits of both dictated free-text reports and standard, structured reports

An Open Source Software Culture in the Undergraduate Computer Science Curriculum

Open source software has made inroads into mainstream computing where it was once the territory of software altruists, and the open source culture of technological collegiality and accountability may benefit education as well as industry. This paper describes the Recourse project, which seeks to transform the computer science undergraduate curriculum through teaching methods based on open source principles, values, ethics, and tools. Recourse differs from similar projects by bringing the open source culture into the curriculum comprehensively, systematically, and institutionally. The current state of the project is described, and initial results from a pilot exercise are presented

GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks

GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop. When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust the force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing and complying with FAIR principles, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of around 160 automated unit tests that examine nearly 530 test files to ensure that the program is running as expected. The GRNsight application (http://dondi.github.io/GRNsight/) and code (https://github.com/dondi/GRNsight) are available under the open source BSD license

Teleradiology as a Foundation for an Enterprise-wide Health Care Delivery System

An effective, integrated telemedicine system has been developed that allows (a) teleconsultation between local primary health care providers (primary care physicians and general radiologists) and remote imaging subspecialists and (b) active patient participation related to his or her medical condition and patient education. The initial stage of system development was a traditional teleradiology consultation service between general radiologists and specialists; this established system was expanded to include primary care physicians and patients. The system was developed by using a well-defined process model, resulting in three integrated modules: a patient module, a primary health care provider module, and a specialist module. A middle agent layer enables tailoring and customization of the modules for each specific user type. Implementation by using Java and the Common Object Request Broker Architecture standard facilitates platform independence and interoperability. The system supports (a) teleconsultation between a local primary health care provider and an imaging subspecialist regardless of geographic location and (b) patient education and online scheduling. The developed system can potentially form a foundation for an enterprise-wide health care delivery system. In such a system, the role of radiologist specialists is enhanced from that of a diagnostician to the management of a patient’s process of care