http://www.aejournal.net The most accessed research articles published by Automated Experimentation 2010-02-15T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Protein–protein interactions form the basis for a vast majority of cellular events, including signal transduction and transcriptional regulation. It is now understood that the study of interactions between cellular macromolecules is fundamental to the understanding of biological systems. Interactions between proteins have been studied through a number of high-throughput experiments and have also been predicted through an array of computational methods that leverage the vast amount of sequence data generated in the last decade. In this review, I discuss some of the important computational methods for the prediction of functional linkages between proteins. I then give a brief overview of some of the databases and tools that are useful for a study of protein–protein interactions. I also present an introduction to network theory, followed by a discussion of the parameters commonly used in analysing networks, important network topologies, as well as methods to identify important network components, based on perturbations. http://www.aejournal.net/content/2/1/2 Karthik Raman Automated Experimentation 2010, 2:2 2010-02-15T00:00:00Z doi:10.1186/1759-4499-2-2 Automated Experimentation 1759-4499 2 2 2010-02-15T00:00:00Z XML We review the main components of autonomous scientific discovery, and how they lead to the concept of a Robot Scientist. This is a system which uses techniques from artificial intelligence to automate all aspects of the scientific discovery process: it generates hypotheses from a computer model of the domain, designs experiments to test these hypotheses, runs the physical experiments using robotic systems, analyses and interprets the resulting data, and repeats the cycle. We describe our two prototype Robot Scientists: Adam and Eve. Adam has recently proven the potential of such systems by identifying twelve genes responsible for catalysing specific reactions in the metabolic pathways of the yeast Saccharomyces cerevisiae. This work has been formally recorded in great detail using logic. We argue that the reporting of science needs to become fully formalised and that Robot Scientists can help achieve this. This will make scientific information more reproducible and reusable, and promote the integration of computers in scientific reasoning. We believe the greater automation of both the physical and intellectual aspects of scientific investigations to be essential to the future of science. Greater automation improves the accuracy and reliability of experiments, increases the pace of discovery and, in common with conventional laboratory automation, removes tedious and repetitive tasks from the human scientist. http://www.aejournal.net/content/2/1/1 Andrew Sparkes Wayne Aubrey Emma Byrne Amanda Clare Muhammed Khan Maria Liakata Magdalena Markham Jem Rowland Larisa Soldatova Kenneth Whelan Michael Young Ross King Automated Experimentation 2010, 2:1 2010-01-04T00:00:00Z doi:10.1186/1759-4499-2-1 Automated Experimentation 1759-4499 2 1 2010-01-04T00:00:00Z XML Background: eCAT is an electronic lab notebook (ELN) developed by Axiope Limited. It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook. Results: During the development of the beta version feedback was incorporated from many groups including the FDA's Center for Biologics Evaluation & Research, Uppsala University, Children's Hospital Boston, Alex Swarbrick's lab at the Garvan Institute in Sydney and Martin Spitaler at Imperial College. More than 100 individuals and groups worldwide then participated in the beta testing between September 2008 and June 2009. The generally positive response is reflected in the following quote about how one lab is making use of eCAT: "Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments." Conclusion: By developing eCAT in close collaboration with lab scientists, Axiope has come up with a practical and easy-to-use product that meets the need of scientists to manage, store and share data online. eCAT is already being perceived as a product that labs can continue to use as their data management and sharing grows in scale and complexity. http://www.aejournal.net/content/1/1/4 Nigel Goddard Rory Macneil Jonathan Ritchie Automated Experimentation 2009, 1:4 2009-10-29T00:00:00Z doi:10.1186/1759-4499-1-4 Automated Experimentation 1759-4499 1 4 2009-10-29T00:00:00Z XML The means we use to record the process of carrying out research remains tied to the concept of a paginated paper notebook despite the advances over the past decade in web based communication and publication tools. The development of these tools offers an opportunity to re-imagine what the laboratory record would look like if it were re-built in a web-native form. In this paper I describe a distributed approach to the laboratory record based which uses the most appropriate tool available to house and publish each specific object created during the research process, whether they be a physical sample, a digital data object, or the record of how one was created from another. I propose that the web-native laboratory record would act as a feed of relationships between these items. This approach can be seen as complementary to, rather than competitive with, integrative approaches that aim to aggregate relevant objects together to describe knowledge. The potential for the recent announcement of the Google Wave protocol to have a significant impact on realizing this vision is discussed along with the issues of security and provenance that are raised by such an approach. http://www.aejournal.net/content/1/1/3 Cameron Neylon Automated Experimentation 2009, 1:3 2009-10-29T00:00:00Z doi:10.1186/1759-4499-1-3 Automated Experimentation 1759-4499 1 3 2009-10-29T00:00:00Z XML With massive amounts of data being generated in electronic format, there is a need in basic science laboratories to adopt new methods for tracking and analyzing data. An electronic laboratory notebook (ELN) is not just a replacement for a paper lab notebook, it is a new method of storing and organizing data while maintaining the data entry flexibility and legal recording functions of paper notebooks. Paper notebooks are regarded as highly flexible since the user can configure it to store almost anything that can be written or physically pasted onto the pages. However, data retrieval and data sharing from paper notebooks are labor intensive processes and notebooks can be misplaced, a single point of failure that loses all entries in the volume. Additional features provided by electronic notebooks include searchable indices, data sharing, automatic archiving for security against loss and ease of data duplication. Furthermore, ELNs can be tasked with additional functions not commonly found in paper notebooks such as inventory control. While ELNs have been on the market for some time now, adoption of an ELN in academic basic science laboratories has been lagging. Issues that have restrained development and adoption of ELN in research laboratories are the sheer variety and frequency of changes in protocols with a need for the user to control notebook configuration outside the framework of professional IT staff support. In this commentary, we will look at some of the issues and experiences in academic laboratories that have proved challenging in implementing an electronic lab notebook. http://www.aejournal.net/content/1/1/5 Jerry Wright Automated Experimentation 2009, 1:5 2009-11-19T00:00:00Z doi:10.1186/1759-4499-1-5 Automated Experimentation 1759-4499 1 5 2009-11-19T00:00:00Z XML Practicing and studying automated experimentation may benefit from philosophical reflection on experimental science in general. This paper reviews the relevant literature and discusses central issues in the philosophy of scientific experimentation. The first two sections present brief accounts of the rise of experimental science and of its philosophical study. The next sections discuss three central issues of scientific experimentation: the scientific and philosophical significance of intervention and production, the relationship between experimental science and technology, and the interactions between experimental and theoretical work. The concluding section identifies three issues for further research: the role of computing and, more specifically, automating, in experimental research, the nature of experimentation in the social and human sciences, and the significance of normative, including ethical, problems in experimental science. http://www.aejournal.net/content/1/1/2 Hans Radder Automated Experimentation 2009, 1:2 2009-10-29T00:00:00Z doi:10.1186/1759-4499-1-2 Automated Experimentation 1759-4499 1 2 2009-10-29T00:00:00Z XML Modern experimental science provides more opportunities for yet larger series of experiments. Demand for experimental results also has become more diverse, requiring results that have direct connections to systems outside the laboratory. With this has come an ability to automate many areas of experimental science, not only the experiments themselves but also the larger processes that contribute to experimentation and analysis more broadly. As automated experimentation becomes more widely used and understood, we launch this journal to provide a proper publication channel for this new breed of interdisciplinary research as well as a bridge to all significant groundwork research that would facilitate possible automated experimentation. With this in mind, we are interested in publishing all kinds of research into scientific experimentation, including research where the potential for automation is at proof or concept or early deployment stage. http://www.aejournal.net/content/1/1/1 David Robertson Siu-wai Leung Dietlind Gerloff Automated Experimentation 2009, 1:1 2009-10-29T00:00:00Z doi:10.1186/1759-4499-1-1 Automated Experimentation 1759-4499 1 1 2009-10-29T00:00:00Z XML