Search results for "INFORMATICS"

The ten grand challenges of synthetic life

2011

The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life i…

Exploring the Effect of Teaching Methods on Students’ Learning of School Informatics

2015

School informatics is a relatively new subject in comparison to mathematics and science. As a result, there is much less research on the area of informatics didactics. Likewise, there is lack of theoretical grounding of the field and associated teaching methods and learning processes. The lack of research in the field of school informatics makes it difficult to identify which methods are effective to teach the subject. In addition, despite the emphasis on a set of well-defined topics, the informatics curriculum makes few suggestions as to which didactical skills teachers need to acquire in order to teach these topics. In fact, school informatics education is still in its infancy. It lacks t…

Protein data condensation for effective quaternary structure classification

2007

Many proteins are composed of two or more subunits, each associated with different polypeptide chains. The number and the arrangement of subunits forming a protein are referred to as quaternary structure. The quaternary structure of a protein is important, since it characterizes the biological function of the protein when it is involved in specific biological processes. Unfortunately, quaternary structures are not trivially deducible from protein amino acid sequences. In this work, we propose a protein quaternary structure classification method exploiting the functional domain composition of proteins. It is based on a nearest neighbor condensation technique in order to reduce both the porti…

2020

Abstract Background and objective Deep learning approaches are common in image processing, but often rely on supervised learning, which requires a large volume of training images, usually accompanied by hand-crafted labels. As labelled data are often not available, it would be desirable to develop methods that allow such data to be compiled automatically. In this study, we used a Generative Adversarial Network (GAN) to generate realistic B-mode musculoskeletal ultrasound images, and tested the suitability of two automated labelling approaches. Methods We used a model including two GANs each trained to transfer an image from one domain to another. The two inputs were a set of 100 longitudina…

Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows

2020

AbstractMany computer-aided design tools are available for synthetic biology and metabolic engineering. Yet, these tools can be difficult to apprehend, sometimes requiring a level of expertise that limits their use by a wider community. Furthermore, some of the tools, although complementary, rely on different input and output formats and cannot communicate with one another. Scientific workflows address these shortcomings while offering a novel design strategy. Among the workflow systems available, Galaxy is a web-based platform for performing findable and accessible data analyses for all scientists regardless of their informatics expertise, along with interoperable and reproducible computat…

Indexing a sequence for mapping reads with a single mismatch

2014

Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure in time and space and can answer subsequent queries in time. Here, n is the length of the s…

An Online Observer for Minimization of Pulsating Torque in SMPM Motors.

2015

A persistent problem of surface mounted permanent magnet (SMPM) motors is the non-uniformity of the developed torque. Either the motor design or the motor control needs to be improved in order to minimize the periodic disturbances. This paper proposes a new control technique for reducing periodic disturbances in permanent magnet (PM) electro-mechanical actuators, by advancing a new observer/estimator paradigm. A recursive estimation algorithm is implemented for online control. The compensating signal is identified and added as feedback to the control signal of the servo motor. Compensation is evaluated for different values of the input signal, to show robustness of the proposed method.

Evaluation of the registration of temporal series of contrast-enhanced perfusion magnetic resonance 3D images of the liver.

2011

The registration of 2D and 3D images is one of the key tasks in medical image processing and analysis. Accurate registration is a crucial preprocessing step for many tasks; consequently, the evaluation of its accuracy becomes necessary. Unfortunately, this is a difficult task, especially when no golden pattern (true result) is available and when the signal values may have changed between successive images to be registered. This is the case this paper deals with: we have a series of 3D images, magnetic resonance images (MRI) of the liver and adjacent areas that have to be registered. They have been taken while a contrast is diffused through the liver tissue, so intensity of each observed poi…

Missing values in deduplication of electronic patient data

2011

Data deduplication refers to the process in which records referring to the same real-world entities are detected in datasets such that duplicated records can be eliminated. The denotation ‘record linkage’ is used here for the same problem.1 A typical application is the deduplication of medical registry data.2 3 Medical registries are institutions that collect medical and personal data in a standardized and comprehensive way. The primary aims are the creation of a pool of patients eligible for clinical or epidemiological studies and the computation of certain indices such as the incidence in order to oversee the development of diseases. The latter task in particular requires a database in wh…

A Large-Scale Empirical Evaluation of Cross-Validation and External Test Set Validation in (Q)SAR.

2013

(Q)SAR model validation is essential to ensure the quality of inferred models and to indicate future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to accept the (Q)SAR model, and to approve its use in real world scenarios as alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model, in particular whether to employ variants of cross-validation or external test set validation, is still under discussion. In this paper, we empirically compare a k-fold cross-validation with external test set validation. To this end we introduce a workflow allowing to realistically simulate t…