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One of the challenges of the Biotechnology industry is keeping up to date with the rapid pace of change and that much of the information, which students learn in their undergraduate studies, will be out of date in a few years. It is therefore crucial that Biotechnology students have the skills to access the relevant information for their studies and critically evaluate the vast volume of information and its sources. By developing information literacy skills, which are part of lifelong learning, Biotechnology graduates are better prepared for their careers. Students also need to understand the issues related to the use of information such as social, political, ethical, and legal implications. This paper will outline the embedding of information literacy skills within the Biotechnology degree at the University of South Australia. Examples of specific activities and their link to assessment will be discussed. [ABSTRACT FROM AUTHOR]

A bioinformatics laboratory exercise based on inherited human morphological traits is presented. It teaches how morphological characters can be used to study the evolutionary history of humans using parsimony. The exercise can easily be used in a pen-and-paper laboratory, but if computers are available, a more versatile analysis can be carried out. The exercise introduces students to the basics of bioinformatics laboratory work, shows them possible problems associated in data acquisition, and most importantly, teaches them basic group working skills, such as the appropriate distribution of work. An open and student-oriented approach, in which group work is designed to support the learning of individual students, was adapted. The exercise is devised in two sessions that cover collection of data, analysis using parsimony, and a combined matrix analysis in a parsimony framework. The exercise, or parts of it, has successfully been applied in bioinformatics courses intended for second to third year biology majors and in adult education. [ABSTRACT FROM AUTHOR]

DNA microarray is an ordered grid containing known sequences of DNA, which represent many of the genes in a particular organism. Each DNA sequence is unique to a specific gene. This technology enables the researcher to screen many genes from cells or tissue grown in different conditions. We developed an undergraduate lecture and laboratory exercise using an interdisciplinary approach to the study of microarray technology. What made this approach unique was studying the evolution of the technology leading up to the formation of the MicroArray Quality Control Project (MAQC). Students realized that this technique has potential of saving lives, making it absolutely necessary to validate all results. Students were then able to complete their own microarray project, evaluate their results and continue to analyze a gene from the study, by further utilizing basic bioinformatic tools as well as critiquing primary journal articles. [ABSTRACT FROM AUTHOR]

This report describes a linked series of Masters-level computer practical workshops. They comprise an advanced functional genomics investigation, based upon analysis of a microarray dataset probing yeast DNA damage responses. The workshops require the students to analyse highly complex transcriptomics datasets, and were designed to stimulate active learning through experience of current research methods in bioinformatics and functional genomics. They seek to closely mimic a realistic research environment, and require the students first to propose research hypotheses, then test those hypotheses using specific sections of the microarray dataset. The complexity of the microarray data provides students with the freedom to propose their own unique hypotheses, tested using appropriate sections of the microarray data. This research latitude was highly regarded by students and is a strength of this practical. In addition, the focus on DNA damage by radiation and mutagenic chemicals allows them to place their results in a human medical context, and successfully sparks broad interest in the subject material. In evaluation, 79% of students scored the practical workshops on a five-point scale as 4 or 5 (totally effective) for student learning. More broadly, the general use of microarray data as a 'student research playground' is also discussed. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 6, pp. 440-447, 2011 [ABSTRACT FROM AUTHOR]

Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option. Furthermore, we believe that a true interdisciplinary science experience would be best served by introduction of bioinformatics modules within existing courses in biology and chemistry and other complementary departments. To that end, with support from the Howard Hughes Medical Institute, we have developed over a dozen independent bioinformatics modules for our students that are incorporated into courses ranging from general chemistry and biology, advanced specialty courses, and classes in complementary disciplines such as computer science, mathematics, and physics. These activities have largely promoted active learning in our classrooms and have enhanced student understanding of course materials. Herein, we describe our program, the activities we have developed, and assessment of our endeavors in this area. [ABSTRACT FROM AUTHOR]

This article describes a new approach to teaching bioinformatics using Arabidopsis genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bloinformatics, using Arabidopsis leucine-rich repeat receptor-like kinase (LRR RLK) genetic sequences. In these exercises, students are asked to explore the intimate relationship between the structure and functions of LRR RLKs and to understand the diverse signaling roles of LRR RLKs in Arabidopsis. Students are also required to identify LRR RLK paralogs and orthologs and to analyze their evolutionary and functional relationships using bioinformatics software. Through these exercises, students are expected to gain the ability to search databases to retrieve genetic data and analyze them using a variety of bioinformatics tools. [ABSTRACT FROM AUTHOR]

The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an understanding of mathematical and physical concepts, an ability to apply these concepts to MBB, and a proficiency with the computational tools and skills related to bioinformatics. We hypothesized that a greater exposure to bioinformatics methods, more rigorous requirements in math and computer science, and a constant demand for integrating information in hands-on laboratory courses would help students develop better analytical skills. Indeed, the assessment data support these predictions. Interestingly, 80% of MBB majors apply and are accepted into graduate schools. [ABSTRACT FROM AUTHOR]

We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students' background knowledge of hemoglobin and chymotrypsin, and foster a better understanding of how protein sequence relates to structure and function. [ABSTRACT FROM AUTHOR]

Studies of metabolism usually evoke memories of densely written wall charts of metabolic pathways of enormous complexity, such as the IUBMB-Nicholson metabolic pathways map or the Roche metabolic pathways wall chart. Advances in bioinformatics in the past decade have brought about a revolution in the way the information in metabolic pathways is viewed and managed. Today, metabolic pathways are stored in knowledge bases that can be queried, modified, copied, and extended with ease, precision, and speed. Moreover, the flexibility of the digital medium for the presentation of metabolic pathways surpasses the traditional printed form used in classical pathway maps. In digital presentations, the separation of the content from the visual presentation is the norm, implying that metabolic pathway maps can be generated dynamically from the information stored in the knowledge base. The most advanced metabolic pathways databases are freely available over the Internet, and this has important implications for modern studies of metabolic pathways in biochemistry and molecular biology. This study reviews two such databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the BioCyc collection of pathway/genome data- bases. The background information and the structure of these databases are presented, with the emphasis on BioCyc, which represents a global multicollaborative effort to unify the representation of metabolic pathways. [ABSTRACT FROM AUTHOR]

PyMOL is a molecular modeling program that can be used in a wide range of studies within the scientific community. Its ability to produce informative, detailed, stereoscopic images makes it a very powerful tool both in the laboratory and in the classroom. However, the PyMOL user interlace is difficult to use, and the PyMOL User's Manual readily admits that ‘development has been focused on capabilities, not on ease-of-use for new users.’ To resolve this, we set out to develop a new interface for PyMOL that helps eliminate the need for command line interactions, making it a much more user-friendly interlace. We have created a tabbed interface called EZ-Viz, which contains a series of buttons and entry fields that allow users to select given attributes of a molecule and make changes to it by clicking a button as opposed to issuing highly syntactical commands. Other features of the interface include a Chime/PyMOL command converter, nine preset molecular views, four molecular movies, and molecular sequence and hetero atom information, all at the click of a button. The ongoing and continued development of EZ-Viz could help to further the use of PyMOL, which we believe to be one of the most powerful molecular viewing programs currently available. [ABSTRACT FROM AUTHOR]

Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private and academic) with a need for bachelor of science students with bioinformatics skills. In consideration of this need, described here is a problem-based class in which students are asked to design a set of intrageneric primers for PCR. The exercise is divided into five classes of 1 h each, in which students use freeware bioinformatics tools and data bases available through the Internet. Besides designing the set of primers, the students will consequently learn the significance and use of the major bioinformatics procedures, such as searching a data base, conducting and analyzing sequence multialignment, comparing sequences with a data base, and selecting primers. [ABSTRACT FROM AUTHOR]

This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled Biomolecular Structure and Bioinformatics. Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics approach that relies on access to the Internet and biological databases. This was an ambitious approach considering that the students mostly had a biological background. There were also time constraints of eight lectures in total and two accompanying practical sessions. The main challenge was that students had to be introduced to computer programming from a beginner level and in a short time provided with enough knowledge to independently solve a simple bioinformatics problem. This was accomplished with a problem directly relevant to the rest of the subject, concerned with the structure-function relationships and experimental techniques for the determination of macromolecular structure. [ABSTRACT FROM AUTHOR]

This article discusses exploring protein function and evolution using free online bioinformatics tools. Bioinformatics provides a set of powerful research tools for predicting the function of a newly discovered protein and has quickly become an important field of training at many universities and medical institutions. The following laboratory exercise highlights the successful integration of bioinformatics into the undergraduate laboratory setting. Teachers teach the protein structure unit of a bioinformatics course first developed at the University of Wisconsin-La Crosse 4 years ago. The course is taught in a computer laboratory twice a year to about 40 students; thus they have modified and refined this exercise over eight course offerings. In the first part of the course, students are assigned an amino acid sequence for an unknown protein. Each student then uses bioinformatics programs in Biology Workbench to analyze the primary amino acid sequence to make several predictions.

Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material over the Internet. Currently, we provide two fully computer-based courses, "Introduction to Bioinformatics" and "Bioinformatics in Functional Genomics." Here we will discuss the application of distance learning in bioinformatics training and our experiences gained during the 3 years that we have run the courses, with about 400 students from a number of universities. The courses are available at bioinf.uta.fi. [ABSTRACT FROM AUTHOR]

The article focuses on the importance of information literacy as a research tool for the students to create interesting work related to life sciences. Here, the author asserts that the literacy is very useful adjuncts to the students in building literacy skills and integration of the concepts. The author further discusses the disadvantages of the information assessment including the validity and reliability of the source and the detailed evaluation of the data to explore the ability of the students in researching educational cases.