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     

Waisel, Y., Eshel, A., Kafkafi, U., eds. Plant roots - the hidden half

Research on plant roots represents an exciting and intriguingfield of science. Undoubtedly, the vast major ity of researcherswithin the field are familiar with the first (1991) and second(1996) editions of this book. Since these editions were published,understanding of root biology has been advanced by using molecularbiology methods and molecular genetic tools which offer novelperspectives for the exploitation and understanding of rootstructure and root processes. The third edition of Plant roots– the hidden half includes revised and expanded informationon topics covered in the previous editions, as well as in     

The UK Human Genome Mapping Project online computing service

This paper presents an overview of computing and networkingfacilities developed by the Medical Research Council to provideonline computing support to the Human Genome Mapping Project(HGMP) in the UK. The facility is connected to a number of othercomputing facilities in various centres of genetics and molecularbiology research excellence, either directly via high-speedlinks or through national and international wide–areanetworks. The paper describes the design and implementationof the current system, a ‘client/server’ networkof Sun, IBM, DEC and Apple servers, gateways and workstations.A short outline of online computing services currently deliveredby this system to the UK human genetics research community isalso provided. More information about the services and theiravailability could be obtained by a direct approach to the UKHGMP-RC.     

Evolutionary Novelties: How Fish Have Built a Heater Out of Muscle

The evolution of any complex morphology or physiological adaptationinvolves the historical transformation of numerous interactingcomponents from an ancestral to a derived state. How such transformationsoccur are central to our understanding of how novel morphologiesarise. The rapid explosion of technology in the field of molecularbiology provides new tools that can be incorporated into studiesexamining the origin of novel phenotypes. Molecular biologicaltechniques can now be used to probe how changes in gene expressionresult in pathways leading to novel or altered morphologies.The integration of molecular approaches into problems in organismalbiology provides a promising new direction for the analysisof form and function. Interdisciplinary studies, combining theresolving power of molecular biologywith the complex problemsof organismal biology, will shed new light on whole animal functionand evolution.     

Use of animation in teaching cell biology

To address the different learning styles of students, and because students can access animation from off-campus computers, the use of digital animation in teaching cell biology has become increasingly popular. Sample processes from cell biology that are more clearly presented in animation than in static illustrations are identified. The value of animation is evaluated on whether the process being taught involves motion, cellular location, or sequential order of numerous events. Computer programs for developing animation and animations associated with cell biology textbooks are reviewed, and links to specific examples of animation are given. Finally, future teaching tools for all fields of biology will increasingly benefit from an expansion of animation to the use of simulation. One purpose of this review is to encourage the widespread use of animations in biology teaching by discussing the nature of digital animation.     

ORBIT: an integrated environment for user-customized bioinformatics tools

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.     

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

Background  

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke.     

Remote access to ACNUC nucleotide and protein sequence databases at PBIL

The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases served by the Pôle Bio-Informatique Lyonnais includes the EMBL, GenBank, RefSeq and UniProt nucleotide and protein sequence databases and a series of other sequence databases that support comparative genomics analyses: HOVERGEN and HOGENOM containing families of homologous protein-coding genes from vertebrate and prokaryotic genomes, respectively; Ensembl and Genome Reviews for analyses of prokaryotic and of selected eukaryotic genomes. This report describes the main features of the ACNUC system and the access to ACNUC databases from any internet-connected computer. Such access was made possible by the definition of a remote ACNUC access protocol and the implementation of Application Programming Interfaces between the C, Python and R languages and this communication protocol. Two retrieval programs for ACNUC databases, Query_win, with a graphical user interface and raa_query, with a command line interface, are also described. Altogether, these bioinformatics tools provide users with either ready-to-use means of querying remote sequence databases through a variety of selection criteria, or a simple way to endow application programs with an extensive access to these databases. Remote access to ACNUC databases is open to all and fully documented (http://pbil.univ-lyon1.fr/databases/acnuc/acnuc.html).     

Normal Pathways: Controlling Isotopes and Building Biomedical Research in Postwar France

During the late 1940s and 1950s, radioisotopes became important resources for biological and medical research. This article explores the strategies used by French researchers to get access to this material, either from the local Atomic Energy Commission (CEA) or from suppliers in the United States or United Kingdom. It focuses on two aspects of this process: the transatlantic circulation of both isotopes and associated instrumentation; the regulation of use and access by the administrative bodies governing research in France. Analyzing the investigations conducted within laboratories associated either with the atomic energy agency or with the local National Institute of Health (INH), the paper discusses the part played by the new tools in the postwar transformation of biomedical research. It contrasts the INH successful development of biological studies and metabolic tracing with the mixed results of CEA in advancing cancer radiotherapy, thus highlighting locally defined “normal paths” to radiobiology.     

A computational study of liposome logic: towards cellular computing from the bottom up

In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in “top-down” synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of “bottom-up” liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie’s stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up.     

HIV/AIDS programmes should focus on improved access

This paper discusses the need for HIV/AIDS programs in sub-Saharan countries to focus more on improved access to information to empower poor people living in remote areas. It is noted that despite Glaxo Wellcome's move to reduce the cost of antiretroviral therapy, it is unlikely to have an impact on most of those infected with or affected by HIV/AIDS, since concerns regarding lack of sustainability, bureaucratic administration, and communication difficulties predominate in the country. In this regard, it is therefore recommended that national HIV/AIDS programs be balanced with the needs of both the community and the individual and in prevention and care. Health workers should be explicit in confronting traditional beliefs, such as those about gender roles and traditional medicine, in prevention campaigns. Moreover, there is also an urgent need to improve access to condoms; strengthen health programs such as directly observed treatment short-term (DOTS) courses for tuberculosis and the syndromic approach to sexually transmitted disease treatment; and improve practical support to communities caring for those who are sick and the orphans. Lastly, all partners working with prevention programs should use the more positive community attitudes towards HIV/AIDS issues seen in many sub-Saharan countries to develop evidence-based programs that focus more on improved access and less on sustainability.     

SEED Servers: High-Performance Access to the SEED Genomes,Annotations, and Metabolic Models

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users.     

植物分子生物学研究极具前景的模式系统--小立碗藓

小立碗藓作为植物分子生物学研究极具前景的模式系统已日益受到人们的重视,它的生活史周期短,易于培养,转基因植株易于分析,核基因组容易和外源DNA发生同源重组,这些特点使它成为研究基因功能的良好材料.一些成功的基因敲除和基因破坏已经在小立碗藓中实现,这些基因的功能也通过小立碗藓转化植株的特点得以证实.小立碗藓标签突变文库已经建立,其应用为小立碗藓基因的进一步研究打下了基础.关于小立碗藓的ESTs数据库已经建立,已有67 000条ESTs信息.     

MacSECPROT: Two programs in basic to evaluate protein secondary structure

Two interactive programs in BASIC are described, which provide useful tools to evaluate protein secondary structure. Output is given in two formats: (1) graphics are displayed on screen, which can be printed immediately, and (2) textfiles are saved to disk as permanent records and can be printed with a word-processing program. The programs are fast and easy to use and could be a valuable teaching aid in biochemical and molecular biology courses. Program lists are written in Microsoft® BASIC for the Apple® Macintosh™, but can be adapted to other machines accepting graphic commands.     

An RNA Phage Lab: MS2 in Walter Fiers’ Laboratory of Molecular Biology in Ghent, from Genetic Code to Gene and Genome, 1963–1976

The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück’s phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers’ laboratory at Ghent University (Belgium) and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his ‘RNA phage lab’ with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s.     

Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes

Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.     

Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut?

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement.     

Integrated prediction of the effect of mutations on multiple protein characteristics

Site-directed mutagenesis is routinely used in modern biology to elucidate the functional or biophysical roles of protein residues, and plays an important role in the field of rational protein design. Over the past decade, a number of computational tools have been developed that can predict the effect of point mutations on a protein's biophysical characteristics. However, these programs usually provide predictions for only a single characteristic. Furthermore, online versions of these tools are often impractical to use for examination of large and diverse sets of mutants. We have created a new web application, (http://enzyme.ucd.ie/PEAT_SA), that can simultaneously predict the effect of mutations on stability, ligand affinity and pK(a) values. PEAT-SA also provides an expanded feature-set with respect to other online tools which includes the ability to obtain predictions for multiple mutants in one submission. As a result, researchers who use site-directed mutagenesis can access state-of-the-art protein design methods with a fraction of the effort previously required. The results of benchmarking PEAT-SA on standard test-sets demonstrate that its accuracy for all three prediction types compares well to currently available tools. We illustrate PEAT-SA's potential by using it to investigate the influence of mutations on the activity of Subtilisin BPN'. This example demonstrates how the ability to obtain a wide range of information from one source, that can be combined to obtain deeper insight into the influence of mutations, makes PEAT-SA a valuable service to both experimental and computational biologists.     

Recent initiatives for radiation oncology resident education in radiation and cancer biology

Nearly all residents from accredited radiation oncology residency programs in the United States are required to take the American College of Radiology (ACR) In-Training examination each year. The test is comprised of three sections: Clinical Radiation Oncology, Radiological Physics, and Radiation (and Cancer) Biology. Here we provide an update on changes to the biology portion of the ACR exam. We also discuss the availability and use of the ACR and biology practice exams as assessment and teaching tools for both the instructors of radiation and cancer biology and the residents they teach.     

Bioinformatics software resources

This review looks at internet archives, repositories and lists for obtaining popular and useful biology and bioinformatics software. Resources include collections of free software, services for the collaborative development of new programs, software news media and catalogues of links to bioinformatics software and web tools. Problems with such resources arise from needs for continued curator effort to collect and update these, combined with less than optimal community support, funding and collaboration. Despite some problems, the available software repositories provide needed public access to many tools that are a foundation for analyses in bioscience research efforts.