Introduction to bioinformatics

Awareness and Predictors of the Use of Bioinformatics in Genome Research in Saudi Arabia

Background

With the advances in genomics research, many countries still need more bioinformatics skills. This study aimed to assess the levels of awareness of bioinformatics and predictors of its use in genomics research among scientists in Saudi Arabia.

Methods

In a cross-sectional survey, 309 scientists of different biological and biomedical specialties were subjected to a previously validated e-questionnaire to collect data on (1) Knowledge about bioinformatics programming languages and tools, (2) Attitude toward acceptance of bioinformatics resources in genome-related research, and (3) The pattern of information-seeking to online bioinformatics resources. Logistic regression analysis was applied to identify the predictors of using bioinformatics in research. Significance was set at p<0.05.

Results

More than one-half (248, 56.4%) of all scientists reported a lack of bioinformatics knowledge. Most participants had a neutral attitude toward bioinformatics (295, 95.4%). The barriers facing acceptance of bioinformatics tools reported were; lack of training (210, 67.9%), insufficient support (180, 58.2%), and complexity of software (138, 44.6%). The limited experience was reported in; having one or more bioinformatics tools (98, 31.7%), using a supercomputer in their research inside (44, 14.2%) and outside Saudi Arabia (55, 17.8%), the need for developing a program to solve a biological problem (129, 41.7%), working in one or more fields of bioinformatics (93, 30.1%), using web applications (112, 36.2%), and using programming languages (102, 33.0%). Significant predictors of conducting genomics research were; younger scientists (p=0.039), Ph.D. education (p=0.003), more than five years of experience (p<0.05), previous training (p<0.001), and higher bioinformatics knowledge scores (p<0.001).

Conclusion

The study revealed a short knowledge, a neutral attitude, a lack of resources, and limited use of bioinformatics resources in genomics research. Education and training during each education level and during the job is recommended. Cloud-based resources may help scientists do research using publicly available Omics data. Further studies are necessary to evaluate collaboration among bioinformatics software developers and biologists.

Hidden in the Middle: Culture, Value and Reward in Bioinformatics

Bioinformatics - the so-called shotgun marriage between biology and computer science - is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised 'outputs' in academia are often defined and rewarded by discipline. Bioinformatics, as an interdisciplinary bricolage, incorporates experts from various disciplinary cultures with their own distinct ways of working. Perceived problems of interdisciplinarity include difficulties of making explicit knowledge that is practical, theoretical, or cognitive. But successful interdisciplinary research also depends on an understanding of disciplinary cultures and value systems, often only tacitly understood by members of the communities in question. In bioinformatics, the 'parent' disciplines have different value systems; for example, what is considered worthwhile research by computer scientists can be thought of as trivial by biologists, and vice versa. This paper concentrates on the problems of reward and recognition described by scientists working in academic bioinformatics in the United Kingdom. We highlight problems that are a consequence of its cross-cultural make-up, recognising that the mismatches in knowledge in this borderland take place not just at the level of the practical, theoretical, or epistemological, but also at the cultural level too. The trend in big, interdisciplinary science is towards multiple authors on a single paper; in bioinformatics this has created hybrid or fractional scientists who find they are being positioned not just in-between established disciplines but also in-between as middle authors or, worse still, left off papers altogether.

Domain knowledge and data quality perceptions in genome curation work

Purpose

– The purpose of this paper is to understand genomics scientists’ perceptions in data quality assurances based on their domain knowledge.

Design/methodology/approach

– The study used a survey method to collect responses from 149 genomics scientists grouped by domain knowledge. They ranked the top-five quality criteria based on hypothetical curation scenarios. The results were compared using χ2 test.

Findings

– Scientists with domain knowledge of biology, bioinformatics, and computational science did not reach a consensus in ranking data quality criteria. Findings showed that biologists cared more about curated data that can be concise and traceable. They were also concerned about skills dealing with information overloading. Computational scientists on the other hand value making curation understandable. They paid more attention to the specific skills for data wrangling.

Originality/value

– This study takes a new approach in comparing the data quality perceptions for scientists across different domains of knowledge. Few studies have been able to synthesize models to interpret data quality perception across domains. The findings may help develop data quality assurance policies, training seminars, and maximize the efficiency of genome data management.

Developing a Library Collection in Bioinformatics

This chapter provides guidelines for developing a university library collection for bioinformatics programs. The chapter discusses current research and scholarly communication trends in bioinformatics and their impact on information needs and information seeking behavior of bioinformaticians and, consequently, on collection development. It also discusses the criteria for making collection development decisions that are largely influenced by the interdisciplinary nature of the field. The types of information resources most frequently used by bioinformaticians are described, specific resources are suggested, and creative options aimed at finding ways for a bioinformatics library collection to expand in the digital era are explored. The author draws on literature in bioinformatics and the library and information sciences as well as on her ten years of experience providing bioinformatics user services at George Mason University. The chapter is geared towards practicing librarians who are charged with developing a collection for bioinformatics academic programs as well as future librarians taking courses on collection development and academic librarianship.

Establishing a master's degree programme in bioinformatics: challenges and opportunities

The development of the Bioinformatics MS degree program at the University of Illinois, the challenges and opportunities associated with such a process, and the current structure of the program is described. This program has departed from earlier University practice in significant ways. Despite the existence of several interdisciplinary programs at the University, a few of which grant degrees, this is the first interdisciplinary program that grants degrees and formally recognises departmental specialisation areas. The program, which is not owned by any particular department but by the Graduate College itself, is operated in a franchise-like fashion via several departmental concentrations. With four different colleges and many more departments involved in establishing and operating the program, the logistics of the operation are of considerable complexity but result in significant interactions across the entire campus.