Modelling Cell Cycle using Different Levels of Representation

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study

Instances and connectors : issues for a second generation process language

This work is supported by UK EPSRC grants GR/L34433 and GR/L32699Over the past decade a variety of process languages have been defined, used and evaluated. It is now possible to consider second generation languages based on this experience. Rather than develop a second generation wish list this position paper explores two issues: instances and connectors. Instances relate to the relationship between a process model as a description and the, possibly multiple, enacting instances which are created from it. Connectors refers to the issue of concurrency control and achieving a higher level of abstraction in how parts of a model interact. We believe that these issues are key to developing systems which can effectively support business processes, and that they have not received sufficient attention within the process modelling community. Through exploring these issues we also illustrate our approach to designing a second generation process language.Postprin

Instances and connectors : issues for a second generation process language

This work is supported by UK EPSRC grants GR/L34433 and GR/L32699Over the past decade a variety of process languages have been defined, used and evaluated. It is now possible to consider second generation languages based on this experience. Rather than develop a second generation wish list this position paper explores two issues: instances and connectors. Instances relate to the relationship between a process model as a description and the, possibly multiple, enacting instances which are created from it. Connectors refers to the issue of concurrency control and achieving a higher level of abstraction in how parts of a model interact. We believe that these issues are key to developing systems which can effectively support business processes, and that they have not received sufficient attention within the process modelling community. Through exploring these issues we also illustrate our approach to designing a second generation process language.Postprin

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

The State Of Play: A Notional Machine for Learning Programming

Comprehension of programming and programs is known to be a difficult task for many beginning students, with many computing courses showing significant drop out and failure rates. In this paper, we present a new notional machine de- sign and implementation to help with understanding of pro- gramming and its dynamics for beginning learners. The no- tional machine offers an abstraction of the physical machine designed for comprehension and learning purposes. We in- troduce the notional machine and a graphical notation for its representation. We also present Novis, an implementation of a dynamic real-time visualiser of this notional machine, integrated into BlueJ

Developing efficient web-based GIS applications

There is an increase in the number of web-based GIS applications over the recent years. This paper describes different mapping technologies, database standards, and web application development standards that are relevant to the development of web-based GIS applications. Different mapping technologies for displaying geo-referenced data are available and can be used in different situations. This paper also explains why Oracle is the system of choice for geospatial applications that need to handle large amounts of data. Wireframing and design patterns have been shown to be useful in making GIS web applications efficient, scalable and usable, and should be an important part of every web-based GIS application. A range of different development technologies are available, and their use in different operating environments has been discussed here in some detail

Scholarly insight Spring 2018: a Data wrangler perspective

In the movie classic Back to the Future a young Michael J. Fox is able to explore the past by a time machine developed by the slightly bizarre but exquisite Dr Brown. Unexpectedly by some small intervention the course of history was changed a bit along Fox’s adventures. In this fourth Scholarly Insight Report we have explored two innovative approaches to learn from OU data of the past, which hopefully in the future will make a large difference in how we support our students and design and implement our teaching and learning practices. In Chapter 1, we provide an in-depth analysis of 50 thousands comments expressed by students through the Student Experience on a Module (SEAM) questionnaire. By analysing over 2.5 million words using big data approaches, our Scholarly insights indicate that not all student voices are heard. Furthermore, our big data analysis indicate useful potential insights to explore how student voices change over time, and for which particular modules emergent themes might arise. In Chapter 2 we provide our second innovative approach of a proof-of-concept of qualification path way using graph approaches. By exploring existing data of one qualification (i.e., Psychology), we show that students make a range of pathway choices during their qualification, some of which are more successful than others. As highlighted in our previous Scholarly Insight Reports, getting data from a qualification perspective within the OU is a difficult and challenging process, and the proof-of-concept provided in Chapter 2 might provide a way forward to better understand and support the complex choices our students make. In Chapter 3, we provide a slightly more practically-oriented and perhaps down to earth approach focussing on the lessons-learned with Analytics4Action. Over the last four years nearly a hundred modules have worked with more active use of data and insights into module presentation to support their students. In Chapter 3 several good-practices are described by the LTI/TEL learning design team, as well as three innovative case-studies which we hope will inspire you to try something new as well. Working organically in various Faculty sub-group meetings and LTI Units and in a google doc with various key stakeholders in the Faculties, we hope that our Scholarly insights can help to inform our staff, but also spark some ideas how to further improve our module designs and qualification pathways. Of course we are keen to hear what other topics require Scholarly insight. We hope that you see some potential in the two innovative approaches, and perhaps you might want to try some new ideas in your module. While a time machine has not really been invented yet, with the increasing rich and fine-grained data about our students and our learning practices we are getting closer to understand what really drives our students

Using High-Rising Cities to Visualize Performance in Real-Time

For developers concerned with a performance drop or improvement in their software, a profiler allows a developer to quickly search and identify bottlenecks and leaks that consume much execution time. Non real-time profilers analyze the history of already executed stack traces, while a real-time profiler outputs the results concurrently with the execution of software, so users can know the results instantaneously. However, a real-time profiler risks providing overly large and complex outputs, which is difficult for developers to quickly analyze. In this paper, we visualize the performance data from a real-time profiler. We visualize program execution as a three-dimensional (3D) city, representing the structure of the program as artifacts in a city (i.e., classes and packages expressed as buildings and districts) and their program executions expressed as the fluctuating height of artifacts. Through two case studies and using a prototype of our proposed visualization, we demonstrate how our visualization can easily identify performance issues such as a memory leak and compare performance changes between versions of a program. A demonstration of the interactive features of our prototype is available at https://youtu.be/eleVo19Hp4k.Comment: 10 pages, VISSOFT 2017, Artifact: https://github.com/sefield/high-rising-city-artifac