21st European Workshop for Rheumatology Research, Vienna, Austria, 1–4 March 2001

Major advances in technology now drive how we approach questions in immunology, particularly in analyzing complex data sets commonly encountered in genomics and proteomics studies. Active areas of investigation include development of novel technologies, identification of elusive target antigens for RA and other diseases, dissection of signaling pathways connecting the lymphocyte cell surface with the nucleus, and exploration of new avenues for therapeutic interventions. The European Workshop for Rheumatology Research (EWRR) is a forum for many European and non-European scientists to present research findings of high quality. Arthritis researchers from around the globe should be strongly encouraged to attend future meetings, the next of which is the 22^nd EWRR meeting in Leiden, the Netherlands, in 2002.     

The biological sciences in India: Aiming high for the future

India is gearing up to become an international player in the life sciences, powered by its recent economic growth and a desire to add biotechnology to its portfolio. In this article, we present the history, current state, and projected future growth of biological research in India. To fulfill its aspirations, India''s greatest challenge will be in educating, recruiting, and supporting its next generation of scientists. Such challenges are faced by the US/Europe, but are particularly acute in developing countries that are racing to achieve scientific excellence, perhaps faster than their present educational and faculty support systems will allow.India, like China, has been riding a rising economic wave. At the time of writing this article, four Indians rank among the ten wealthiest individuals in the world, and the middle class is projected to rise to 40% of the population by 2025 (Farrell and Beinhocker, 2007). Even with the present global economic setbacks, India''s economy is expected to grow to become the third largest in the world. India''s recent economic boom has been driven largely by its service and information technology industries, fueled to a large extent by jobs provided by multinational companies. However, this “outsourcing” model is unlikely to persist indefinitely. India''s future must rely upon its own capacity for innovation, which will require considerable investment in education and research.Biotechnology represents a potential sector of economic growth and an important component in India''s national health agenda. Appreciating the important role that biology will play in this century, the Indian government is expanding as well as starting several new biological research institutes, which will open up many new positions for life science researchers. Funds also are becoming available for state-of-the-art equipment, thus decreasing the earlier large disparity in support facilities between the top research institutes in India and the US/Europe. India is becoming an increasingly viable location to conduct biological research and a fertile ground for new biotechnology companies. However, success need not rise in proportion to money invested, unless India attracts and supports its best young people to do research.Many academic centers and industries in the US/Europe are beginning to have an eye on India, the world''s largest democratic country, for possible collaborations. Western institutions have long benefited from having Indian scientists on their faculty or postdoctoral fellows/graduate students in their laboratories (perhaps benefitting more than India itself). However, Western scientists, by and large, know very little about the scientific and educational systems in India. (As was true of authors of this article before we began our 8-month sabbatical at the National Center for Biological Sciences in Bangalore). The goal of this article is to provide a brief historical and contemporary view of the biological sciences in India. We also provide an editorial perspective on the upcoming challenges for the Indian life sciences, with a particular emphasis on how India will grow and support its next generation of scientific leaders.     

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.     

Modelling,abstraction, and computation in systems biology: A view from computer science

Systems biology is centrally engaged with computational modelling across multiple scales and at many levels of abstraction. Formal modelling, precise and formalised abstraction relationships, and computation also lie at the heart of computer science—and over the past decade a growing number of computer scientists have been bringing their discipline's core intellectual and computational tools to bear on biology in fascinating new ways. This paper explores some of the apparent points of contact between the two fields, in the context of a multi-disciplinary discussion on conceptual foundations of systems biology.     

Workshops: A Great Way to Enhance and Supplement a Degree

As part of the International Society for Computational Biology Student Council (ISCB-SC), Regional Student Groups (RSGs) have helped organise workshops in the emerging fields of bioinformatics and computational biology. Workshops are a great way for students to gain hands-on experience and rapidly acquire knowledge in advanced research topics where curriculum-based education is yet to be developed. RSG workshops have improved dissemination of knowledge of the latest bioinformatics techniques and resources among student communities and young scientists, especially in developing nations. This article highlights some of the benefits and challenges encountered while running RSG workshops. Examples cover a variety of subjects, including introductory bioinformatics and advanced bioinformatics, as well as soft skills such as networking, career development, and socializing. The collective experience condensed in this article is a useful starting point for students wishing to organise their own tailor-made workshops.     

Essential Bioinformatics * Jin Xiong * Cambridge University Press; ISBN: 0-521-60082-0; 339pp.; 2006; * {pound}65.00 (hardcover); {pound}29.00 (paperback).

Few would argue the need for today's college biology majorsto have basic skills in bioinformatics. Yet, their undergraduatefaculty faces several challenges in providing these skills,particularly at smaller colleges. First, faculty members whoteach bioinformatics have usually been trained in molecularbiology, genetics or biochemistry. Therefore, most do not haveextensive applied mathematics experience beyond statistics.Second, bioinformatics textbooks for undergraduate biology majorsare rare. Most bioinformatics books are geared to researchers,computer programmers or graduate students. Others are simpleuser manuals, with little coverage of critical evaluation ofthe output. Third, most students today have great ‘point-and-click’computing skills, but minimal understanding or patience forcommand-line computing or programming. In light of these challenges to introducing undergraduate studentsto bioinformatics, it was quite a joy to read and review ProfessorJin Xiong's recent book, Essential Bioinformatics. This compact,economical, first edition of     

Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations

In this paper we introduce Armadillo v1.1, a novel workflow platform dedicated to designing and conducting phylogenetic studies, including comprehensive simulations. A number of important phylogenetic and general bioinformatics tools have been included in the first software release. As Armadillo is an open-source project, it allows scientists to develop their own modules as well as to integrate existing computer applications. Using our workflow platform, different complex phylogenetic tasks can be modeled and presented in a single workflow without any prior knowledge of programming techniques. The first version of Armadillo was successfully used by professors of bioinformatics at Université du Quebec à Montreal during graduate computational biology courses taught in 2010-11. The program and its source code are freely available at: .     

The origins of bioinformatics

Bioinformatics is often described as being in its infancy, but computers emerged as important tools in molecular biology during the early 1960s. A decade before DNA sequencing became feasible, computational biologists focused on the rapidly accumulating data from protein biochemistry. Without the benefits of super computers or computer networks, these scientists laid important conceptual and technical foundations for bioinformatics today.     

Visualizing the knowledge structure and evolution of bioinformatics

Background

Bioinformatics has gained much attention as a fast growing interdisciplinary field. Several attempts have been conducted to explore the field of bioinformatics by bibliometric analysis, however, such works did not elucidate the role of visualization in analysis, nor focus on the relationship between sub-topics of bioinformatics.

Results

First, the hotspot of bioinformatics has moderately shifted from traditional molecular biology to omics research, and the computational method has also shifted from mathematical model to data mining and machine learning. Second, DNA-related topics are bridge topics in bioinformatics research. These topics gradually connect various sub-topics that are relatively independent at first. Third, only a small part of topics we have obtained involves a number of computational methods, and the other topics focus more on biological aspects. Fourth, the proportion of computing-related topics hit a trough in the 1980s. During this period, the use of traditional calculation methods such as mathematical model declined in a large proportion while the new calculation methods such as machine learning have not been applied in a large scale. This proportion began to increase gradually after the 1990s. Fifth, although the proportion of computing-related topics is only slightly higher than the original, the connection between other topics and computing-related topics has become closer, which means the support of computational methods is becoming increasingly important for the research of bioinformatics.

Conclusions

The results of our analysis imply that research on bioinformatics is becoming more diversified and the ranking of computational methods in bioinformatics research is also gradually improving.

     

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Prof. Haruki Nakamura, who is the former head of Protein Data Bank Japan (PDBj) and an expert in computational biology, retired from Osaka University at the end of March 2018. He founded PDBj at the Institute for Protein Research, together with other faculty members, researchers, engineers, and annotators in 2000, and subsequently established the worldwide Protein Data Bank (wwPDB) in 2003 to manage the core archive of the Protein Data Bank (PDB), collaborating with RCSB-PDB in the USA and PDBe in Europe. As the former head of PDBj and also an expert in structural bioinformatics, he has grown PDBj to become a well-known data center within the structural biology community and developed several related databases, tools and integrated with new technologies, such as the semantic web, as primary services offered by PDBj.     

Bayesian methods in bioinformatics and computational systems biology

Bayesian methods are valuable, inter alia, whenever there is a need to extract information from data that are uncertain or subject to any kind of error or noise (including measurement error and experimental error, as well as noise or random variation intrinsic to the process of interest). Bayesian methods offer a number of advantages over more conventional statistical techniques that make them particularly appropriate for complex data. It is therefore no surprise that Bayesian methods are becoming more widely used in the fields of genetics, genomics, bioinformatics and computational systems biology, where making sense of complex noisy data is the norm. This review provides an introduction to the growing literature in this area, with particular emphasis on recent developments in Bayesian bioinformatics relevant to computational systems biology.     

Report on 2nd Royan Institute International Summer School on Developmental Biology and Stem Cells Tehran,Iran, 17–22nd July 2011

The 2nd Royan Institute International Summer School was built around the topic of stem cells and grounding in the discipline of developmental biology. The meeting provided not only direct transfer of technical and intellectual information, the normal process in scientific meetings, but was also a forum for the exchange of personal ideas of science as a creative pursuit. This summer school introduced aspiring young Iranian scientists to international researchers and exposed the latter to a rich culture that highly values learning and education, attested by the confident, intelligent young men and women who asked probing questions and who were eager to participate in the workshops. Hossein Baharvand's dedication and passion for science have led to an impressive record of national and international peer-reviewed publications and an increasing number of students who pursue science in Iran, and shows how the right people can create an environment where good science, good science education and motivation will flourish. This report summarizes some of the activities of the workshop in the Royan Institute and the impressions of the visiting scientists in the wider context of the scientific and cultural heritage of Iran.     

Saline Systems: A research journal bridging gene systems and ecosystems

Saline Systems addresses the publication needs of scientists conducting basic and applied research on coastal and inland saline environments and their flora and fauna. The journal covers research at all levels, from individual genes to whole genomes and entire ecosystems. Rapid progress in the molecular biology and microbial ecology of halotolerant and halophilic organisms and the sensitivity of many saline environments warrants an online journal with fast turnaround times. Many saline environments are threatened and the need for an Open Access journal to address the dissemination and sharing of knowledge on their conservation and management is compelling. Saline Systems provides an interdisciplinary forum for scientists working within all of the relevant fields.     

Integration of evidence across human and model organism studies: A meeting report

The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance use disorders (SUDs), computational biology, and FAIR (Findability, Accessibility, Interoperability, and Reusability) data sharing. The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs. Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline future steps to support more effective collaboration—particularly between animal model research communities and human genetics and clinical research teams. This review summarizes key facets of this catalytic discussion with a focus on new opportunities and gaps in resources and knowledge on SUDs.     

蜜蜂全基因组出笼前后

在2006年10月26日,期待已久的蜜蜂的基因组序列在英国杂志《自然》上发表了。这一事件对于全世界蜜蜂生物学家来说,标志着蜜蜂研究“后基因组时代”的开始。这一重大项目由倍乐医学院完成,耗资800万美元,历时2年。而实际上对于基因组的注释又经过近2年的时间,由代表15个国家、来自64个实验室的170名科学家完成。这一等待是值得的基因组序列最终发表后,生物学家通过互联网能做他们自己的“数据采掘”,用这一可得的公共资源验证自己的假说。事实上,在蜜蜂基因组文章在《自然》上发表的当周,其姊妹刊上发表的约50篇相关论文中,有一半以上是基于生物信息学的研究,这些刊物包括《科学》、《基因组研究》、《美国国家科学院院报》及《昆虫分子生物学》。蜜蜂与人类享有一些共性劳动分工,复杂的通信系统包括语言,发达的保卫和防御系统,精妙的建筑以及为了共同利益自我牺牲的特点。由于有这些共性,蜜蜂基因组的发表将使科学家不仅能够深入研究蜜蜂生物学,而且能深入了解我们人类自身的生物学。     

生物信息学数据库调查分析及其利用研究

从生物信息学数据库利用的角度调查分析生物信息学数据库的现状,为我国科研人员利用网上生物信息学数据库以及生物信息中心的开发提供科学依据和参考价值。研究采用网上调查的方法,对法国生物信息中心Infobiogen建立维护的生物信息学数据库目录DBcat中收录的511个数据库进行调查统计,分析其类型分布、国家分布、更新频率和获取方式;在此基础上。进一步利用欧洲分子生物学信息网(EMBnet)中30个成员国节点对生物信息学数据库利用现状进行统计分析。     

Software agents in molecular computational biology

Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations.     

Investment in plant research and development bears fruit in China

Recent rapid progress in plant science and biotechnology in China demonstrates that China’s stronger support for funding in plant research and development (R&D) has borne fruit. Chinese groups have contributed major advances in a range of fields, such as rice biology, plant hormone and developmental biology, genomics and evolution, plant genetics and epigenetics, as well as plant biotechnology. Strigolactone studies including those identifying its receptor and dissecting its complex structure and signaling are representative of the recent researches from China at the forefront of the field. These advances are attributable in large part to interdisciplinary studies among scientists from plant science, chemistry, bioinformatics, structural biology, and agronomy. The platforms provided by national facilities facilitate this collaboration. As well, efficient restructuring of the top–down organization of state programs and free exploration of scientists’ interests have accelerated achievements by Chinese researchers. Here, we provide a general outline of China’s progress in plant R&D to highlight fields in which Chinese research has made significant contributions.     

Learning genetics through an authentic research simulation in bioinformatics

Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process by solving a problem in the context of authentic research in genetics. Through the learning environment, the learners are exposed to a genetics problem which was developed on the basis of research in which a mutated gene, which causes deafness, was identified. They follow, step by step, the way scientists try to solve it, using the current geneticists' toolbox. The environment uses an adapted version of the BLAST program (a bioinformatics tool which enables to find similarities between sequences), which was modified in a way that enables the teachers and students to use it easily. Using quantitative and qualitative research approaches, we were able to show that learning through the bioinformatics environment promotes construction of new knowledge structures and influences students' acquisition of a deeper and multidimensional understanding of the genetics domain. In addition, learning through the bioinformatics environment influences students' comprehension of the practices and scientific ways of thinking.