Computational Biology and Bioinformatics in Nigeria

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.     

Biomedicine and naturopathic healing in West Germany a historical and ethnomedical view of a stormy relationship

We trace the history of medical pluralism in Germany from the perspective of a clinically oriented medical anthropology. The continuation of naturopathic medicine in both formal and informal health care illumines fundamental epistemological issues. Cultural and social forces in Germany shaped the scientific and technical development of medicine, which continues in a form distinctly different from that of medicine in North America. The construction of clinical reality in German practice is distinctive and edifying for a crosscultural understanding of medical systems of knowledge and praxis.A part of this article draws on Seidler 1983. Maretzki's research was carried out under a grant from the Fulbright Kommission, Germany, We acknowledge with appreciation the encouragement and support by colleagues at Albert-Ludwigs Universitaet, Freiburg, and in other German universities, by physicians in private practice who responded to our request for an interview, by physicians and others in different Kur institutions throughout West Germany, and, importantly, the help of patients in answering questions, We also appreciate the helpful comments on earlier drafts of this article by Atwood Gaines and Charles Leslie, Special appreciation goes to Arthur Kleinman for his stimulating encouragement and patient editorial assistance.     

生物信息学本科专业建设现状

随着后基因组时代的到来,生物信息学逐渐进入了黄金发展期。生物信息学教育体系的建立和完善是永葆生物信息学活力的关键。国际和国内的生物信息学本科专业建设情况的分析显示全球生物信息学本科教育均处于起始阶段。深刻剖析了内蒙古自治区生物信息发展的瓶颈问题以及内蒙古科技大学开设生物信息学本科专业的优势和必要性。未来,随着测序技术、计算机技术等的进步,生物信息学将继续蓬勃发展;生物信息学人才的需求将不断扩大。为适应人才市场的需求,预计会有越来越多的高等院校将加入到中国的生物信息学本科教育事业。     

生物信息学本科人才培养的调研与思考

近年来,生物信息学已经逐步发展成为现代生物学和医学等领域的关键技术方法,社会对生物信息学专业人才的需求不断扩大,生物信息学的本科教育也受到了越来越多的关注和重视。为了探索更加合理的人才培养模式、完善课程设置和教学计划,本文以中美两国开设生物信息学本科专业的高校为对象,分别选取一些代表高校并进行深入调研,对比分析课程设置和人才培养现状。结果显示,生物信息学的跨学科性质在各高校中均得到一定体现,培养学生具有多元化的知识结构已经成为生物信息学人才培养的一项共识。同时,根据调研的结果,也对国内生物信息学本科教育提出一些启发与建议。     

BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training

The completion of the human genome project, and other genome sequencing projects, has spearheaded the emergence of the field of bioinformatics. Using computer programs to analyse DNA and protein information has become an important area of life science research and development. While it is not necessary for most life science researchers to develop specialist bioinformatic skills (including software development), basic skills in the application of common bioinformatics software and the effective interpretation of results are increasingly required by all life science researchers. Training in bioinformatics is increasingly occurring within the university system as part of existing undergraduate science and specialist degrees. One difficulty in bioinformatics education is the sheer number of software programs required in order to provide a thorough grounding in the subject to the student. Teaching requires either a well-maintained internal server with all the required software, properly interfacing with student terminals, and with sufficient capacity to handle multiple simultaneous requests, or it requires the individual installation and maintenance of every piece of software on each computer. In both cases, there are difficult issues regarding site maintenance and accessibility. In this article, we discuss the use of BioManager, a web-based bioinformatics application integrating a variety of common bioinformatics tools, for teaching, including its role as the main bioinformatics training tool in some Australian and international universities. We discuss some of the issues with using a bioinformatics resource primarily created for research in an undergraduate teaching environment.     

Patenting of university and non-university public research organisations in Germany: evidence from patent applications for medical research results

Background

Patents are one of the most important forms of intellectual property. They grant a time-limited exclusivity on the use of an invention allowing the recuperation of research costs. The use of patents is fiercely debated for medical innovation and especially controversial for publicly funded research, where the patent holder is an institution accountable to public interest. Despite this controversy, for the situation in Germany almost no empirical information exists. The purpose of this study is to examine the amount, types and trends of patent applications for health products submitted by German public research organisations.

Methods/Principal Findings

We conducted a systematic search for patent documents using the publicly accessible database search interface of the German Patent and Trademark Office. We defined keywords and search criteria and developed search patterns for the database request. We retrieved documents with application date between 1988 and 2006 and processed the collected data stepwise to compile the most relevant documents in patent families for further analysis. We developed a rationale and present individual steps of a systematic method to request and process patent data from a publicly accessible database. We retrieved and processed 10194 patent documents. Out of these, we identified 1772 relevant patent families, applied for by 193 different universities and non-university public research organisations. 827 (47%) of these patent families contained granted patents. The number of patent applications submitted by universities and university-affiliated institutions more than tripled since the introduction of legal reforms in 2002, constituting almost half of all patent applications and accounting for most of the post-reform increase. Patenting of most non-university public research organisations remained stable.

Conclusions

We search, process and analyse patent applications from publicly accessible databases. Internationally mounting evidence questions the viability of policies to increase commercial exploitation of publicly funded research results. To evaluate the outcome of research policies a transparent evidence base for public debate is needed in Germany.     

Emigration,isolation and the slow start of molecular biology in Germany

Until the 1930s Germany had been the international leader in biochemistry, chemistry, and areas of biology. After WWII, however, molecular biology as a new interdisciplinary scientific enterprise was scarcely represented in Germany for almost 20 years. Three major reasons for the low performance of molecular biology are discussed: first, the forced emigration of Jewish scientists after 1933, which not only led to the expulsion of future distinguished molecular biologists, but also to a strong decline of “dynamic biochemistry”, a field which contributed greatly to molecular biology. Second, German university structures that strongly impeded interdisciplinary research. Third, the international isolation and self-isolation of German scientists that was a major obstacle to the implementation of new fields of research developed elsewhere. Despite the fact that there was no official boycott against Germany as there had been after WWI and despite the Cold War policy of integrating Germans into the West, as a consequence of National Socialism and WWI for many years only very few German scientists gained access to the international community of molecular biologists. Max Delbrück played an important role in helping the Germans establish modern, mostly molecular, biology because he retained strong connections to Germany. Most importantly, it required a new generation of young scientists who had received part of their training in the US to establish modern molecular biology at German universities and Max Planck Institutes.     

Using Co-authorship Networks to Map and Analyse Global Neglected Tropical Disease Research with an Affiliation to Germany

Background

Research on Neglected Tropical Diseases (NTDs) has increased in recent decades, and significant need-gaps in diagnostic and treatment tools remain. Analysing bibliometric data from published research is a powerful method for revealing research efforts, partnerships and expertise. We aim to identify and map NTD research networks in Germany and their partners abroad to enable an informed and transparent evaluation of German contributions to NTD research.

Methodology/Principal Findings

A SCOPUS database search for articles with German author affiliations that were published between 2002 and 2012 was conducted for kinetoplastid and helminth diseases. Open-access tools were used for data cleaning and scientometrics (OpenRefine), geocoding (OpenStreetMaps) and to create (Table2Net), visualise and analyse co-authorship networks (Gephi). From 26,833 publications from around the world that addressed 11 diseases, we identified 1,187 (4.4%) with at least one German author affiliation, and we processed 972 publications for the five most published-about diseases. Of those, we extracted 4,007 individual authors and 863 research institutions to construct co-author networks. The majority of co-authors outside Germany were from high-income countries and Brazil. Collaborations with partners on the African continent remain scattered. NTD research within Germany was distributed among 220 research institutions. We identified strong performers on an individual level by using classic parameters (number of publications, h-index) and social network analysis parameters (betweenness centrality). The research network characteristics varied strongly between diseases.

Conclusions/Significance

The share of NTD publications with German affiliations is approximately half of its share in other fields of medical research. This finding underlines the need to identify barriers and expand Germany’s otherwise strong research activities towards NTDs. A geospatial analysis of research collaborations with partners abroad can support decisions to strengthen research capacity, particularly in low- and middle-income countries, which were less involved in collaborations than high-income countries. Identifying knowledge hubs within individual researcher networks complements traditional scientometric indicators that are used to identify opportunities for collaboration. Using free tools to analyse research processes and output could facilitate data-driven health policies. Our findings contribute to the prioritisation of efforts in German NTD research at a time of impending local and global policy decisions.     

The development of human genetics in Germany; a personal view

A personal account is given of the reconstruction and development of human genetics in Germany during the years following World War 2. An important stimulus was funding, as a result of the recognition of the genetic hazards of atomic radiation. Starting from 1960, human genetics institutes were progressively established throughout West Germany; comparable development was later in East Germany because of political factors. The first genetic counselling units were formed in 1972, but molecular biology only became an integral part of human genetics institutes at a relatively late stage. Close international links have characterised post-war human genetics in Germany from the outset and a tradition of close links with developing countries has also been established.     

自然科学课程思政的教学探索——以微生物学为例

课程思政是近年来在我国高校广泛推广的一种新的教学理念,其核心思想是将高校思想政治教育融入到各类课程教学之中。高校课程可以分为思想政治课程、通识教育课程、哲学社会科学课程、自然科学课程,其中自然科学课程与思政教育关系最为松散,思政元素的融入也最为困难。本文从微生物学融入课程思政的教学实践出发,分析高校自然科学类课程实施课程思政的必要性及难点,探索思政资源的挖掘路径,通过调查研究评估课程思政的教学效果,以及对课程思政的实践进行教学反思。此外,对专业课教师关于课程思政的观点分歧也做了初步探讨。本文旨在为微生物学相关课程实施课程思政提供理论支撑、实证数据以及教学经验,并可为其他自然科学类课程参鉴。     

The trade-off between a high and an equal biological standard of living—Evidence from Germany

Following German re-unification, East Germany moved from a state-socialist to a market-based economic system. Using West Germany as a “control group”, we examine how the change affected the level and the equality of the biological standard of living. We find that before unification, East Germany had a lower but somewhat more equally distributed biological standard of living than the West. After unification, East Germany rapidly caught up in terms of height but at the expense of equality. This suggests that a trade-off exists between a high and an equally distributed biological standard of living. Unlike previous research, we find that West Germany's pre-unification height advantage was smallest in towns with 5000-20,000 inhabitants and largest in cities with 20,000-100,000 inhabitants (females) or in cities with more than 100,000 inhabitants (males). Between regions, height converged both in East and West Germany, but particularly markedly among East-German males. Equality convergence, like height convergence, is significantly larger for East than for West-German males.     

GOBLET: The Global Organisation for Bioinformatics Learning,Education and Training

In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.     

Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

Since 2010, the European Molecular Biology Laboratory''s (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students.In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.     

A Review of Undergraduate Evolution Education in U.S. Universities: Building a Unifying Framework

Despite a considerable amount of scientific evidence, evolution is still a highly controversial issue in American education. This review analyzes studies that investigate the relationship between evolution education, the nature of science, and religious beliefs in U.S. universities. We performed a comprehensive literature search focusing on publications that analyzed and compared at least two of the following constructs: understanding of evolutionary theory (ET), acceptance of ET, instruction in ET, prior exposure to ET, religious beliefs, understanding the nature of science, and understanding of scientific theories. Here, we examine publications for consistent relationships among constructs across studies and discuss the most commonly cited education strategies for teaching evolution in higher education. Based on the literature, we find that instruction has a significant and positive effect on acceptance and understanding of ET; acceptance and understanding, however, are not directly related. We also find that the relationship between acceptance of ET and religious beliefs is unclear and needs further research. Through reviewing 15 published studies, we find that the primary problems associated with undergraduate evolution education research are: small sample size, varying methodologies, lack of statistical analysis, inappropriate use of constructs, and lack of continuity among studies. This review exposes the need for a unifying framework and development of experts in this field to investigate and understand the factors that affect evolution education at U.S. universities.     

遗传学课程思政教育的探索与实践

课程思政对高校落实立德树人、实现人才培养目标具有重要的意义。在专业课中进行课程思政改革有助于探究高校专业课程中育人功能的发挥。遗传学是生命科学专业重要的基础课程,在生命科学知识体系的构建中具有重要作用。立足内蒙古农业大学示范课程改革的教学实践,我们重塑了教学目标,改革教学方法,挖掘遗传学课程中蕴含的思政元素,使德育教育深入教师心、学生心,贯穿于教学、教评全过程,使知识传授、能力培养与价值引领同向同行,以提升学生的综合素质。     

Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan

The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computational tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on specific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the development of bioinformatics in the country.     

关于临床医学专业学位硕士研究生教学与培养的几点思考

随着医学科学技术的发展和社会需求的扩大,医学界对高层次人才的需求持续增长。为推进我国医疗卫生系统的可持续发展,医学院校适应时势变化,积极调整和优化研究生教学类型结构,大力发展专业学位研究生教育。专业学位研究生教育以培养临床思维和提高临床技能为重点,同时注重基本科研素质的培养。随着专业学位研究生招生人数的增加,如何保证研究生的"质"和"量"的同步提升成为高校和教育者研究热点。本文通过借鉴临床医学科学学位硕士研究生的教学与培养模式,结合临床医学专业学位硕士研究生的特点及培养要求,对以往教学经验与教训做一总结,着力于探索一条适合临床医学专业学位硕士研究生的教学与培养模式,为建立标准化的临床医学专业学位硕士研究生的教学与培养模式提供参考。     

后基因组时代的生物信息学

随着人类基因组计划的完成,不断积累的巨量的生物学数据和快速发展的信息学技术,给后基因组时代的生物信息学研究带来了新的挑战。该文对后基因组时代的生物信息学研究内容进行了比较全面的描述,分别就其研究对象和研究方向作了区别讨论,分析了生物信息学研究的现状和趋势,比较了国内外的研究发展情况和差距。针对我国在研究中所存在的主要问题,提出了建议并做了展望。