Design and implementation of a genomics field trip program aimed at secondary school students

With the rapid pace of advancements in biological research brought about by the application of computer science and information technology, we believe the time is right for introducing genomics and bioinformatics tools and concepts to secondary school students. Our approach has been to offer a full-day field trip in our research facility where secondary school students carry out experiments at the laboratory bench and on a laptop computer. This experience offers benefits for students, teachers, and field trip instructors. In delivering a wide variety of science outreach and education programs, we have learned that a number of factors contribute to designing a successful experience for secondary school students. First, it is important to engage students with authentic and fun activities that are linked to real-world applications and/or research questions. Second, connecting with a local high school teacher to pilot programs and linking to curricula taught in secondary schools will enrich the field trip experience. Whether or not programs are linked directly to local teachers, it is important to be flexible and build in mechanisms for collecting feedback in field trip programs. Finally, graduate students can be very powerful mentors for students and should be encouraged to share their enthusiasm for science and to talk about career paths. Our experiences suggest a real need for effective science outreach programs at the secondary school level and that genomics and bioinformatics are ideal areas to explore.     

Student test scores are improved in a virtual learning environment

This study evaluates the effectiveness of delivering the core curriculum of an introductory neuroscience course using a software application referred to as a virtual learning interface (VLI). The performance of students in a virtual learning environment (VLE) is compared with that of students in a conventional lecture hall in which the same lecturer presented the same material. This study was not designed to determine whether grades are improved by augmenting a lecture with other information. The VLI takes advantage of audio, video, animation, and text in a multimedia computer environment. Our results indicate that raw average scores on weekly examinations were 14 percentage points higher for students in the VLE compared with those for students in a conventional lecture hall setting. Moreover, normalized test scores were over 5 points higher for students in the VLE. This analysis suggest that a core curriculum can be effectively presented to students using the VLE, thereby making it possible for faculty to spend less class time relaying facts and more time engaging students in discussion of scientific theory.     

An application of multivariate ratio methods for the analysis of a longitudinal clinical trial with missing data.

This paper presents an analysis of a longitudinal multi-center clinical trial with missing data. It illustrates the application, the appropriateness, and the limitations of a straightforward ratio estimation procedure for dealing with multivariate situations in which missing data occur at random and with small probability. The parameter estimates are computed via matrix operators such as those used for the generalized least squares analysis of catetorical data. Thus, the estimates may be conveniently analyzed by asymptotic regression methods within the same computer program which computes the estimates, provided that the sample size is sufficiently computer program which computes the estimates, provided that the sample size is sufficiently large.     

Comparison of different approaches and computer programs for progress curve analysis of enzyme kinetics

For the analysis of enzyme kinetics, a variety of programs exists. These programs apply either algebraic or dynamic parameter estimation, requiring different approaches for data fitting. The choice of approach and computer program is usually subjective, and it is generally assumed that this choice has no influence on the obtained parameter estimates. However, this assumption has not yet been verified comprehensively. Therefore, in this study, five computer programs for progress curve analysis were compared with respect to accuracy and minimum data amount required to obtain accurate parameter estimates. While two of these five computer programs (MS‐Excel, Origin) use algebraic parameter estimation, three computer programs (Encora, ModelMaker, gPROMS) are able to perform dynamic parameter estimation. For this comparison, the industrially important enzyme penicillin amidase (EC 3.5.1.11) was studied, and both experimental and in silico data were used. It was shown that significant differences in the estimated parameter values arise by using different computer programs, especially if the number of data points is low. Therefore, deviations between parameter values reported in the literature could simply be caused by the use of different computer programs.     

The effective time of centrifugation for the analysis of boundary spreading in sedimentation velocity experiments

This investigation establishes a likely order of magnitude for the zero-time correction factor governing the effective time of centrifugation that is pertinent in the analysis of boundary spreading in sedimentation velocity experiments. This correction is shown to be too small to unduly affect the magnitudes of sedimentation and diffusion coefficients deduced from the application of computer software incorporating the printout value of ω2t and an effective position of the air-solution meniscus that is obtained as an additional parameter in the analysis involving nonlinear least-squares curve-fitting of sedimentation velocity distributions to the Lamm equation. Although this procedure slightly underestimates the actual meniscus position (r(a)), uncertainty about its exact location precludes adoption of the alternative approach with r(a) fixed and the correction to ω2t regarded as the additional curve-fitting parameter.     

Generation and visualization of root-like structures in a three-dimensional space

In his Notebooks Leonardo da Vinci describes his diameter squared rule for the branching of above-ground tree parts. We now apply this branching-rule to the study of root-branching. Repeated application of this rule in a recursive computer program (ArtRoot) produces the diameters of the branches. An algorithm in this recursive program calculates the orientation of the branches in a three-dimensional space. From these data three-dimensional root-like structures are visualized by a computer program (PLUTON) designed to draw three-dimensional molecular structures. The visualization shows that starting from a relatively simple, symmetrical structure of dichotomous branching, more complex, asymmetrical root-like structures arise even if only a few parameter values are changed. The introduction of randomness into parameter values produces structures that differ considerably in their architecture. An extra force has been added in order to influence the orientation of new branches in space and to increase the flexibility of the structure formation.     

Teaching Bioinformatics in Concert

Can biology students without programming skills solve problems that require computational solutions? They can if they learn to cooperate effectively with computer science students. The goal of the in-concert teaching approach is to introduce biology students to computational thinking by engaging them in collaborative projects structured around the software development process. Our approach emphasizes development of interdisciplinary communication and collaboration skills for both life science and computer science students.     

Integrating Interactive Computational Modeling in Biology Curricula

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by “building and breaking it” via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the “Vision and Change” call to action in undergraduate biology education by providing a hands-on approach to biology.     

Teaching computer interfacing with virtual instruments in an object-oriented language.

LabVIEW is a graphic object-oriented computer language developed to facilitate hardware/software communication. LabVIEW is a complete computer language that can be used like Basic, FORTRAN, or C. In LabVIEW one creates virtual instruments that aesthetically look like real instruments but are controlled by sophisticated computer programs. There are several levels of data acquisition VIs that make it easy to control data flow, and many signal processing and analysis algorithms come with the software as premade VIs. In the classroom, the similarity between virtual and real instruments helps students understand how information is passed between the computer and attached instruments. The software may be used in the absence of hardware so that students can work at home as well as in the classroom. This article demonstrates how LabVIEW can be used to control data flow between computers and instruments, points out important features for signal processing and analysis, and shows how virtual instruments may be used in place of physical instrumentation. Applications of LabVIEW to the teaching laboratory are also discussed, and a plausible course outline is given.     

Defining absolute confidence limits in the identification of Caulobacter proteins by peptide mass mapping

A derivatization reaction, guanidination, was recently reported that increases MALDI-TOF MS sensitivity toward lysine-terminated peptides. Its application conveys sequence information that can be used as a parameter in peptide mass mapping database searches. This paper presents a systematic study of the impact of guanidination on proteomic analysis of an entire bacterial organelle. Sixty-two 2-D gel isolated proteins from Caulobacter crescentus stalks were studied. A novel computer algorithm, Prodigies, was developed to analyze the data. Absolute confidence limits associated with protein assignments were established using Monte Carlo simulations of database searches. The advantages of guanidination are illustrated using both experimental and theoretical data.     

Teaching human genetics in biochemistry by computer literature searching.

We describe a new user-intense-learning experience that incorporates the teaching of clinical and research applications of human genetics in biochemistry while training first-year medical students to develop skills in computer access to the literature. Human genetics was incorporated into the biochemistry curriculum by providing each student with experience in on-line literature searching in MEDLINE, using Grateful Med, in order to write an abstract about a specific inherited biochemical disorder. We stressed the need for the students to obtain current information in order to understand and interpret the rapidly changing field of human genetics. We taught the students that the most efficient method of obtaining such information was by searching the medical literature via computer.     

Vergleich der Kot- und Harn-N-Trennung in 2 verschiedenen Ratten-Stoffwechselkäfigsystemen

The energy availability from the feedstuffs and the energy requirement of animals are characterized by the metabolizable energy. The metabolizable energy of the feed (feedstuff, ration) is interpreted as potential energy.

For comparative analyses within and between animal species with regard to the energetic feed value of single feedstuffs the parameter “relative fat retention effect” is introduced.

The metabolizable energy of a ration is estimated in consideration of live weight and protein production (protein in body gain and egg). The energy requirement is calculated factorial ‐ as a rule by the partial utilization of metabolizable energy for partial performances (k_f, k _p, k _o) in connection with the level and kind of partial performance; k _m is not used in the system.

The proposed system of energetic feed evaluation is available as “computer variant” as well as “manual variant”. The computer programme is fitted first of all to application in research and teaching. (The complete documentation of the proposal for energetic feed evaluation for fowls including a diskette for using of the computer programme for scientific application can be claimed in limited extend from the author.)     

The Use of a Symbol Processing Computer Language in Point Estimation of Parameters and in Construction of Confidence Intervals

This paper presents a method to generate automatically computer programs which are necessary for parameter estimation, hypothesis tests and construction of confidence intervals by the maximum likelihood method. The spectral or density function of the random variable is arbitrary, but must be known and given in closed form. The programming language used is the symbol processing language LIBAFORM, whose statements are interpreted by a package of LISP-routines. The application of the method is illustrated by the analysis of a linear model whose residuals follow a logarithmic F-distribution, and the analysis of a dose-response curve.     

Computers in health-sciences education. An application to electrocardiography

Aspects of a computer-based education (CBE) are described. Recent developments in the use of computer in health-sciences education are highlighted. An interactive computer system ( CALE ) has been developed to provide individualised instruction and testing for biomedical and medical sciences students. CALE is a system for computer assisted learning of electrocardiography which consists of an organizer program and few subprograms . The system has a self-instruction mode which is equivalent to lecturing . Moreover, review questions are supplied either in multiple choice questions ( MCQ ) and/or matched questions and answers ( MQA ) forms. Furthermore, the system can stimulate normal as well as abnormal electrocardiograms. A statistical program is included to evaluate the performance of the students while using the CALE -system. A comment file is created so that the users can register their comments about the CALE and the difficulties they have faced in using the system. CALE is easy to use and requires no knowledge of programming. The feedback obtained from the students currently using the system is encouraging. CALE is written in Data General FORTRAN 5.     

Can a tablet device alter undergraduate science students' study behavior and use of technology?

This article reports findings from a study investigating undergraduate biological sciences students' use of technology and computer devices for learning and the effect of providing students with a tablet device. A controlled study was conducted to collect quantitative and qualitative data on the impact of a tablet device on students' use of devices and technology for learning. Overall, we found that students made extensive use of the tablet device for learning, using it in preference to laptop computers to retrieve information, record lectures, and access learning resources. In line with other studies, we found that undergraduate students only use familiar Web 2.0 technologies and that the tablet device did not alter this behavior for the majority of tools. We conclude that undergraduate science students can make extensive use of a tablet device to enhance their learning opportunities without institutions changing their teaching methods or computer systems, but that institutional intervention may be needed to drive changes in student behavior toward the use of novel Web 2.0 technologies.     

Teaching cytopathology to second-year medical students. An interactive,case-based approach

OBJECTIVE: To develop and implement an electronic, interactive, case-based cytopathology educational system for second-year medical students. STUDY DESIGN: Ten different learning modules, corresponding to various organ systems in pathology and encompassing the essence of clinical cytopathology, were developed. The modules are software-based, menu-driven, digital programs that are displayed on a computer monitor and can be projected onto a large screen via LCD projectors. Each module takes 15-20 minutes to complete and contains three to four case-based interactive clinical scenarios. Each case contains sequenced, multiple-choice questions with immediate feedback. Each module also includes an atlas mode for viewing all the case images plus additional images to enrich the learning experience. RESULTS: Preliminary feedback from students taking the pathology course has shown encouraging responses. The students enjoyed the practical approach of the modules, finding them easy to use. Their interest level remained high as they discovered how their general medical knowledge could apply to solving real-life clinical cytopathology cases. CONCLUSION: By utilizing these unique instructional modules in the second-year pathology course, medical students learn the application of clinical cytopathology in everyday medical practice. This not only provides them with the theoretical background and morphologic knowledge of the diseases taught but also gives them the ability to apply it in simulated real-life clinical scenarios.     

The Estimation of the Segregation Parameter when Ascertainment is not Complete

Procedures to estimate the genetic segregation parameter when ascertainment of families is incomplete, have previously relied on iterative computer algorithms since estimators with closed form are lacking. We now present the Minimum Variance Unbiased Estimator for the segregation parameter under any ascertainment probability. This estimator assumes a simple form when ascertainment is complete. We also present a simple estimator, akin to Li and Mantel's (1968) estimator, but without the restriction that ascertainment be complete. The performance of these estimators is compared with respect to asymptotic efficiency. We also provide tables that define the required number of families of a given size that need to be sampled to achieve a specific power for testing simple hypothesis on the segregation parameter.     

The evolving role of animal laboratories in physiology instruction

Laboratory exercises are intended to illustrate concepts and add an active learning component to courses. Since the 1980s, there has been a decline in animal laboratories offered in conjunction with medical physiology courses. The most important single reason for this is cost, but other contributing factors include the development of computer simulations, changes in medical education, and pressure from antivivisectionists. Unfortunately, the elimination of animal laboratories has occurred with relatively little consideration of the educational impact of this change. Although computer simulations are considered effective in helping students acquire basic physiological concepts, there is evidence some students acquire a more thorough understanding of the material through the more advanced and challenging experience of an animal laboratory. The fact that such laboratories offer distinct educational advantages should be taken into account when courses are designed.