Sticks, balls or a ribbon? Results of a formative user study with bioinformaticians

User interfaces in modern bioinformatics tools are designed for experts. They are too complicated for\ud novice users such as bench biologists. This report presents the full results of a formative user study as part of a\ud domain and requirements analysis to enhance user interfaces and collaborative environments for\ud multidisciplinary teamwork. Contextual field observations, questionnaires and interviews with bioinformatics\ud researchers of different levels of expertise and various backgrounds were performed in order to gain insight into\ud their needs and working practices. The analysed results are presented as a user profile description and user\ud requirements for designing user interfaces that support the collaboration of multidisciplinary research teams in\ud scientific collaborative environments. Although the number of participants limits the generalisability of the\ud findings, the combination of recurrent observations with other user analysis techniques in real-life settings\ud makes the contribution of this user study novel

Educating the educators: Incorporating bioinformatics into biological science education in Malaysia

Bioinformatics can be defined as a fusion of computational and biological sciences. The urgency to process and analyse the deluge of data created by proteomics and genomics studies has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. In this review, we described the components that constitute the bioinformatics field and distinctive education criteria that are required to produce individuals with bioinformatics training. This paper will also provide an introduction and overview of bioinformatics in Malaysia. The existing bioinformatics scenario in Malaysia was surveyed to gauge its advancement and to plan for future bioinformatics education strategies. For comparison, we surveyed methods and strategies used in education by other countries so that lessons can be learnt to further improve the implementation of bioinformatics in Malaysia. It is believed that accurate and sufficient steerage from the academia and industry will enable Malaysia to produce quality bioinformaticians in the future

myTea: Connecting the Web to Digital Science on the Desktop

Bioinformaticians regularly access the hundreds of databases and tools that are available to them on the Web. None of these tools communicate with each other, causing the scientist to copy results manually from a Web site into a spreadsheet or word processor. myGrids' Taverna has made it possible to create templates (workflows) that automatically run searches using these databases and tools, cutting down what previously took days of work into hours, and enabling the automated capture of experimental details. What is still missing in the capture process, however, is the details of work done on that material once it moves from the Web to the desktop: if a scientist runs a process on some data, there is nothing to record why that action was taken; it is likewise not easy to publish a record of this process back to the community on the Web. In this paper, we present a novel interaction framework, built on Semantic Web technologies, and grounded in usability design practice, in particular the Making Tea method. Through this work, we introduce a new model of practice designed specifically to (1) support the scientists' interactions with data from the Web to the desktop, (2) provide automatic annotation of process to capture what has previously been lost and (3) associate provenance services automatically with that data in order to enable meaningful interrogation of the process and controlled sharing of the results

Phospho.ELM:a database of experimentally verified phosphorylation sites in eukaryotic proteins

BACKGROUND: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.DESCRIPTION: Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.CONCLUSION: Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.</p

Inscribing a discipline: tensions in the field of bioinformatics

Bioinformatics, the application of computer science to biological problems, is a central feature of post-genomic science which grew rapidly during the 1990s and 2000s. Post-genomic science is often high-throughput, involving the mass production of inscriptions [Latour and Woolgar (1986), Laboratory Life: the Construction of Scientific Facts. Princeton, NJ: Princeton University Press]. In order to render these mass inscriptions comprehensible, bioinformatic techniques are employed, with bioinformaticians producing what we call secondary inscriptions. However, despite bioinformaticians being highly skilled and credentialed scientists, the field struggles to develop disciplinary coherence. This paper describes two tensions militating against disciplinary coherence. The first arises from the fact that bioinformaticians as producers of secondary inscriptions are often institutionally dependent, subordinate even, to biologists. With bioinformatics positioned as service, it cannot determine its own boundaries but has them imposed from the outside. The second tension is a result of the interdisciplinary origin of bioinformatics – computer science and biology are disciplines with very different cultures, values and products. The paper uses interview data from two different UK projects to describe and examine these tensions by commenting on Calvert's [(2010) “Systems Biology, Interdisciplinarity and Disciplinary Identity.” In Collaboration in the New Life Sciences, edited by J. N. Parker, N. Vermeulen and B. Penders, 201–219. Farnham: Ashgate] notion of individual and collaborative interdisciplinarity and McNally's [(2008) “Sociomics: CESAGen Multidisciplinary Workshop on the Transformation of Knowledge Production in the Biosciences, and its Consequences.” Proteomics 8: 222–224] distinction between “black box optimists” and “black box pessimists.

Agents in Bioinformatics

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions

Frontiers in Pigment Cell and Melanoma Research

We identify emerging frontiers in clinical and basic research of melanocyte biology and its associated biomedical disciplines. We describe challenges and opportunities in clinical and basic research of normal and diseased melanocytes that impact current approaches to research in melanoma and the dermatological sciences. We focus on four themes: (1) clinical melanoma research, (2) basic melanoma research, (3) clinical dermatology, and (4) basic pigment cell research, with the goal of outlining current highlights, challenges, and frontiers associated with pigmentation and melanocyte biology. Significantly, this document encapsulates important advances in melanocyte and melanoma research including emerging frontiers in melanoma immunotherapy, medical and surgical oncology, dermatology, vitiligo, albinism, genomics and systems biology, epidemiology, pigment biophysics and chemistry, and evolution