Visualisation of the information resources for cell biology

Intelligent multimodal interfaces can facilitate scientists in utilising available information resources. Combining scientific visualisations with interactive and intelligent tools can help create a “habitable” information space. Development of such tools remains largely iterative. We discuss an ongoing implementation of intelligent interactive visualisation of information resources in cell biology

The distorted mirror of Wikipedia: a quantitative analysis of Wikipedia coverage of academics

Activity of modern scholarship creates online footprints galore. Along with traditional metrics of research quality, such as citation counts, online images of researchers and institutions increasingly matter in evaluating academic impact, decisions about grant allocation, and promotion. We examined 400 biographical Wikipedia articles on academics from four scientific fields to test if being featured in the world's largest online encyclopedia is correlated with higher academic notability (assessed through citation counts). We found no statistically significant correlation between Wikipedia articles metrics (length, number of edits, number of incoming links from other articles, etc.) and academic notability of the mentioned researchers. We also did not find any evidence that the scientists with better WP representation are necessarily more prominent in their fields. In addition, we inspected the Wikipedia coverage of notable scientists sampled from Thomson Reuters list of "highly cited researchers". In each of the examined fields, Wikipedia failed in covering notable scholars properly. Both findings imply that Wikipedia might be producing an inaccurate image of academics on the front end of science. By shedding light on how public perception of academic progress is formed, this study alerts that a subjective element might have been introduced into the hitherto structured system of academic evaluation.Comment: To appear in EPJ Data Science. To have the Additional Files and Datasets e-mail the corresponding autho

Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.

BackgroundUsing knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. We showed that embedding the knowledge representation and question-answering abilities in an electronic textbook helped to engage student interest and improve learning. A natural question that arises from this success, and this paper's primary focus, is whether a similar approach is applicable across a range of life science textbooks. To answer that question, we considered four different textbooks, ranging from a below-introductory college biology text to an advanced, graduate-level neuroscience textbook. For these textbooks, we investigated the following questions: (1) To what extent is knowledge shared between the different textbooks? (2) To what extent can the same upper ontology be used to represent the knowledge found in different textbooks? (3) To what extent can the questions of interest for a range of textbooks be answered by using the same reasoning mechanisms?ResultsOur existing modeling and reasoning methods apply especially well both to a textbook that is comparable in level to the text studied in our previous work (i.e., an introductory-level text) and to a textbook at a lower level, suggesting potential for a high degree of portability. Even for the overlapping knowledge found across the textbooks, the level of detail covered in each textbook was different, which requires that the representations must be customized for each textbook. We also found that for advanced textbooks, representing models and scientific reasoning processes was particularly important.ConclusionsWith some additional work, our representation methodology would be applicable to a range of textbooks. The requirements for knowledge representation are common across textbooks, suggesting that a shared semantic infrastructure for the life sciences is feasible. Because our representation overlaps heavily with those already being used for biomedical ontologies, this work suggests a natural pathway to include such representations as part of the life sciences curriculum at different grade levels

"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology

Automatic Recognition of Mammal Genera on Camera-Trap Images using Multi-Layer Robust Principal Component Analysis and Mixture Neural Networks

The segmentation and classification of animals from camera-trap images is due to the conditions under which the images are taken, a difficult task. This work presents a method for classifying and segmenting mammal genera from camera-trap images. Our method uses Multi-Layer Robust Principal Component Analysis (RPCA) for segmenting, Convolutional Neural Networks (CNNs) for extracting features, Least Absolute Shrinkage and Selection Operator (LASSO) for selecting features, and Artificial Neural Networks (ANNs) or Support Vector Machines (SVM) for classifying mammal genera present in the Colombian forest. We evaluated our method with the camera-trap images from the Alexander von Humboldt Biological Resources Research Institute. We obtained an accuracy of 92.65% classifying 8 mammal genera and a False Positive (FP) class, using automatic-segmented images. On the other hand, we reached 90.32% of accuracy classifying 10 mammal genera, using ground-truth images only. Unlike almost all previous works, we confront the animal segmentation and genera classification in the camera-trap recognition. This method shows a new approach toward a fully-automatic detection of animals from camera-trap images

Politically Correct Science: Why Johnny Can’t Read Scientific Creationism

The playing field is far from level in the contest between Evolutionism and Scientific Creationism. Science faculty with ambitions to move up to larger universities are unlikely to assign readings in Creation Science. Scientists who express doubts about Evolutionism are punished for straying from orthodoxy. Scientific publishers are generally unwilling to accept manuscripts from Creationist researchers and theorists. Secular review sources either neglect Creationist works altogether or are so uniformly hostile and dismissive that they are not useful for separating the wheat from the chaff. Unless librarians muster the integrity and professional diligence to collect robustly in Scientific Creationism, a monolithic Evolutionist siege will succeed

Visualizing Morphogenesis through Instability Formation in 4-D Printing.

Heterogeneous growth in a myriad of biological systems can lead to the formation of distinct morphologies during the maturation processes of different species. We demonstrate that the distinct circumferential buckling observed in pumpkins can be reproduced by a core-shell barrel structure using four-dimensional (4D) printing, taking advantage of digital light processing (DLP)-based three-dimensional (3D) printing and stimulus-responsive hydrogels. The mechanical mismatch between the stiff core and compliant shell results in buckling instability on the surface. The initiation and development of the buckling are governed by the ratio of core/shell radius, the ratio of core/shell swelling ratios, and the mismatch between the core and shell in stiffness. Furthermore, the rigid core not only acts as a source of circumferential confinement but also sets a boundary at the poles of the entire structure. The heterogeneous structures with controllable buckling geometrically and structurally behave much like plants' fruits. This replicates the biological morphologic change and elucidates the general mechanism and dynamics of the complex instability formation of heterogeneous 3D objects

Nontrivial quantum effects in biology: A skeptical physicists' view

Invited contribution to "Quantum Aspects of Life", D. Abbott Ed. (World Scientific, Singapore, 2007).Comment: 15 pages, minor typographical errors correcte