Educating the educators: Incorporating bioinformatics into biological science education in Malaysia

Bioinformatics can be defined as a fusion of computational and biological sciences. The urgency to process and analyse the deluge of data created by proteomics and genomics studies has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. In this review, we described the components that constitute the bioinformatics field and distinctive education criteria that are required to produce individuals with bioinformatics training. This paper will also provide an introduction and overview of bioinformatics in Malaysia. The existing bioinformatics scenario in Malaysia was surveyed to gauge its advancement and to plan for future bioinformatics education strategies. For comparison, we surveyed methods and strategies used in education by other countries so that lessons can be learnt to further improve the implementation of bioinformatics in Malaysia. It is believed that accurate and sufficient steerage from the academia and industry will enable Malaysia to produce quality bioinformaticians in the future

Pengembangan Buku Ajar Biologi Sel dengan Pendekatan Bioinformatika

Textbooks are learning guide books used by students in order to help achieve the goals of national education. Development of textbooks is one of the ways in which to facilitate the achievement of learning indicators. Development of Cell Biology textbooks by using bioinformatics approaches Dick and Carey development model. Textbooks developed validated by subject matter experts, instructional media experts, individual testing 15 students, and 15 students were group trial. Validation results matter experts declared feasible by 84% in good categories. The results of the validation study media experts declared feasible by 82.4% in good categories.Buku ajar merupakan buku panduan pembelajaran yang digunakan oleh siswa guna membantu mencapai tujuan pendidikan nasional. Pengembangan buku ajar merupakan salah satu cara yang dilakukan untuk memfasilitasi tercapainya indikator pembelajaran. Pengembangan buku ajar Biologi Sel dengan pendekatan Bioinformatika menggunakan model pengembangan Dick and Carey. Buku ajar yang dikembangkan divalidasi oleh ahli materi, ahli media pembelajaran, 15 mahasiswa uji coba perorangan, dan 15 mahasiswa uji coba kelompok sedang. Hasil validasi ahli materi menyatakan layak sebesar 84% dengan kategori baik. Hasil validasi ahli media pembelajaran menyatakan layak sebesar 82,4% dengan kategori baik

Teaching the Foundations of Data Science: An Interdisciplinary Approach

The astronomical growth of data has necessitated the need for educating well-qualified data scientists to derive deep insights from large and complex data sets generated by organizations. In this paper, we present our interdisciplinary approach and experiences in teaching a Data Science course, the first of its kind offered at the Wright State University. Two faculty members from the Management Information Systems (MIS) and Computer Science (CS) departments designed and co-taught the course with perspectives from their previous research and teaching experiences. Students in the class had mix backgrounds with mainly MIS and CS majors. Students' learning outcomes and post course survey responses suggested that the course delivered a broad overview of data science as desired, and that students worked synergistically with those of different majors in collaborative lab assignments and in a semester long project. The interdisciplinary pedagogy helped build collaboration and create satisfaction among learners.Comment: Presented at SIGDSA Business Analytics Conference 201

PENGEMBANGAN BUKU AJAR BIOLOGI SEL DENGAN PENDEKATAN BIOINFORMATIKA

Textbooks are learning guide books used by students in order to help achieve the goals of national education. Development of textbooks is one of the ways in which to facilitate the achievement of learning indicators. Development of Cell Biology textbooks by using bioinformatics approaches Dick and Carey development model. Textbooks developed validated by subject matter experts, instructional media experts, individual testing 15 students, and 15 students were group trial. Validation results matter experts declared feasible by 84% in good categories. The results of the validation study media experts declared feasible by 82.4% in good categories. Buku ajar merupakan buku panduan pembelajaran yang digunakan oleh siswa guna membantu mencapai tujuan pendidikan nasional. Pengembangan buku ajar merupakan salah satu cara yang dilakukan untuk memfasilitasi tercapainya indikator pembelajaran. Pengembangan buku ajar Biologi Sel dengan pendekatan Bioinformatika menggunakan model pengembangan Dick and Carey. Buku ajar yang dikembangkan divalidasi oleh ahli materi, ahli media pembelajaran, 15 mahasiswa uji coba perorangan, dan 15 mahasiswa uji coba kelompok sedang. Hasil validasi ahli materi menyatakan layak sebesar 84% dengan kategori baik. Hasil validasi ahli media pembelajaran menyatakan layak sebesar 82,4% dengan kategori baik

Using experimental evolution and next-generation sequencing to teach bench and bioinformatic skills

PrePrints 2 Abstract Advances in sequencing technology have exponentially increased data-generating capabilities, 15 and data analysis has now become the major hurdle in many research programs. As sequencing tools become more accessible and automated, experimental design and data analysis skills become the key factors in determining the success of a study. However, proper bioinformatic analysis also relies on a deep understanding of laboratory workflow, in order to prevent biases in the data. This is particularly true if commercial kits are used, as proprietary reagents 20 frequently obfuscate underlying reactions and their conditions. Here we present a training module that seamlessly combines laboratory components (experimental evolution of T5 bacteriophage resistance by Escherichia coli, and library preparation), with bioinformatic analysis of the resulting data. Students conduct a simple genetic variant discovery experiment in the course of about a week. The module uses mature Illumina chemistry for both library 25 preparation and sequencing, though it can be modified for use with any sequencing platform

Development of a BLAST-based command line tool for sequence alignment

This thesis work studies the development of a BLAST (Basic Local Alignment Search Tool) -based command line tool for the use of biological sequence alignment. The focus of the work is in identifying the most important software quality criteria based on the target user base, and how to produce such a program using existing resources as efficiently as possible. The first part of the work covers the basic principles of biological sequence alignment, the BLAST algorithm, and related existing software applications. The next part introduces software quality criteria and typical models for their application. A brief literature review of the state of software development and quality in the field of bioinformatics is included to illustrate the most common problems that one might need to navigate in the development of a program such as the one discussed in this thesis. The second part of the thesis discusses the design of the program, selected quality criteria as well as technical aspects of the development. The results section details the results of the project with an overview of the program architecture. Following this is a discussion on how well the implementation filled the desired software quality criteria and ideas for further development

Strategies for Enhancing Communication Between Students, Academics and Researchers Participating in Large-Scale Undergraduate Research Projects

Spreading the word about science and inspiring people to connect with the processes and outcomes of science, whether as researchers, educators, students, industry professionals or consumers, is essential in forging stronger links among scientists and with the communities that stand to benefit from their work. How do we nurture inspirational scientific communication in the context of university undergraduate science education, particularly in large cohort settings that are often more mind-numbing than soul-stirring? Communicating your own discoveries effectively is the zenith of scientific endeavour. We have developed a large-scale original research experience for second or third year undergraduate biomedical science students. The students undertake ‘mini’ projects and present their research outcomes verbally, visually and in a written format suitable for journal publication. This helps students understand how science works and develops their ability to explain scientific concepts to their peers and others. To promote ‘original research’ to students in ways that inspire and motivate participation, we have also evolved strategies to help instructors and researchers communicate successfully with large student cohorts, including a wiki for secure data storage, FAQ sheets and databases of bioinformatics tools. Introduction of the research experience has improved survey scores overall and on items relating to communication. These strategies are applicable to any course seeking to introduce students to the practice of research and communication of research outcomes. Our experience suggests optimal multidimensional communication may be best achieved through instructors, researchers and students working together to develop effective stratagems for surviving and thriving in the information-dense, digital world

MolabIS: A Labs Backbone for Storing, Managing and Evaluating Molecular Genetics Data

Using paper lab books and spreadsheets to store and manage growing datasets in a file system is inefficient, time consuming and error-prone. Therefore, the overall purpose of this study is to develop an integrated information system for small laboratories conducting Sanger sequencing and microsatellite genotyping projects. To address this, the thesis has investigated the following three issues. First, we proposed a uniform solution using the workflow approach to efficiently collect and store data items in different labs. The outcome is the design of the formalized data framework which is the basic to create a general data model for biodiversity studies. Second, we designed and implemented a web-based information system (MolabIS) allowing lab people to store all original data at each step of their workflow. MolabIS provides essential tools to import, store, organize, search, modify, report and export relevant data. Finally, we conducted a case study to evaluate the performance of MolabIS with typical operations in a production mode. Consequently, we can propose the use of virtual appliance as an efficient solution for the deployment of complex open-source information systems like MolabIS. The major result of this study, along with the publications, is the MolabIS software which is freely released under GPL license at http://www.molabis.org. With its general data model, easy installation process and additional tools for data migration, MolabIS can be used in a wide range of molecular genetics labs