The BioDynaMo Project

2021 ◽  
pp. 1785-1791
Author(s):  
Roman Bauer ◽  
Lukas Breitwieser ◽  
Alberto Di Meglio ◽  
Leonard Johard ◽  
Marcus Kaiser ◽  
...  
Keyword(s):  
Computer Simulations ◽  
Lessons Learned ◽  
Biological Research ◽  
Computing Systems ◽  
Spatial And Temporal Scales ◽  
Scientific Investigations ◽  
Complex Organization ◽  
Computer Resources ◽  
Scientific Questions ◽  
Heterogeneous Interactions

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project aims at a general platform for computer simulations for biological research. Since scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This chapter describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learned by the team during these first stages.

The BioDynaMo Project

2017 ◽  
pp. 117-125 ◽  
Author(s):  
Roman Bauer ◽  
Lukas Breitwieser ◽  
Alberto Di Meglio ◽  
Leonard Johard ◽  
Marcus Kaiser ◽  
...  
Keyword(s):  
Computer Simulations ◽  
Lessons Learned ◽  
Biological Research ◽  
Computing Systems ◽  
Spatial And Temporal Scales ◽  
Scientific Investigations ◽  
Complex Organization ◽  
Computer Resources ◽  
Scientific Questions ◽  
Heterogeneous Interactions

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project aims at a general platform for computer simulations for biological research. Since scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This chapter describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learned by the team during these first stages.

The Small Mammal Project: Engaging Students as Scientists

2017 ◽  
Vol 79 (3) ◽  
pp. 200-206
Author(s):  
Erika V. Iyengar ◽  
Paul T. Meier ◽  
Rachel E. Hamelers
Keyword(s):  
College Courses ◽  
Scientific Process ◽  
Scientific Creativity ◽  
Scientific Investigations ◽  
Hands On ◽  
Upper Level ◽  
Multiple Species ◽  
Dissemination Of Results ◽  
Scientific Questions

This article describes a sustained, student-driven, inquiry-based set of activities meant to illuminate the scientific process from the initial scientific questions to oral dissemination of results. It is appropriate for science majors and nonmajors, advanced high school through upper-level college courses. Involving students in hands-on, self-driven investigations will allow them to see the challenges of quantitative scientific investigations, and the role of scientific creativity in experimental design and interpretation. This project allows a large group of students to engage in the type of research project often only available to students working one-on-one with instructors or in research labs. This activity requires skeletons of multiple species of small mammals, but there are many ways to alter the project to suit available resources. We expect that students involved in hands-on, self-directed scientific investigations early in their academic careers are less likely to view science as a mere accumulation of facts and more likely to be empowered to participate later in more sustained scientific investigations.

scholarly journals A comprehensive, FAIR file format for neuroanatomical structure modeling

2020 ◽  
Author(s):  
A. E. Sullivan ◽  
S. J. Tappan ◽  
P. J. Angstman ◽  
A. Rodriguez ◽  
G. C. Thomas ◽  
...  
Keyword(s):  
Biological Research ◽  
File Format ◽  
Data Types ◽  
Alternative Analysis ◽  
Data Format ◽  
Digital Reconstruction ◽  
Data Files ◽  
Rich Data ◽  
Scientific Questions ◽  
Neuroscience Community

AbstractWith advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, Neuromorphological File Specification (4.0), available at www.mbfbioscience.com/filespecification (Angstman et al. 2020). One of such technologies, the format created and maintained by MBF Bioscience is broadly utilized by the neuroscience community. The data format’s structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological data format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data standards promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al. 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream application and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.

scholarly journals Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic

2021 ◽  
Vol 118 (46) ◽  
pp. e2024891118
Author(s):  
Núria López ◽  
Luigi Del Debbio ◽  
Marc Baaden ◽  
Matej Praprotnik ◽  
Laura Grigori ◽  
...  
Keyword(s):  
Crisis Management ◽  
Computer Simulations ◽  
Lessons Learned ◽  
Mitigation Strategies ◽  
For Profit ◽  
Not For Profit ◽  
Societal Challenges ◽  
The World ◽  
Advanced Computing ◽  
Urgent Computing

PRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations are a pillar of research to assess the risks of different scenarios and investigate mitigation strategies. While the world deals with the subsequent waves of the pandemic, we present a reflection on the use of urgent supercomputing for global societal challenges and crisis management.

scholarly journals User-defined semantics for the design of IoT systems enabling smart interactive experiences

2020 ◽  
Vol 24 (6) ◽  
pp. 781-796
Author(s):  
Carmelo Ardito ◽  
Giuseppe Desolda ◽  
Rosa Lanzilotti ◽  
Alessio Malizia ◽  
Maristella Matera ◽  
...  
Keyword(s):  
User Interaction ◽  
Lessons Learned ◽  
Smart Environments ◽  
Home Automation ◽  
Computing Systems ◽  
Work Activities ◽  
Domain Experts ◽  
Interactive Applications ◽  
Everyday Work ◽  
Iot Devices

AbstractAutomation in computing systems has always been considered a valuable solution to unburden the user. Internet of Things (IoT) technology best suits automation in different domains, such as home automation, retail, industry, and transportation, to name but a few. While these domains are strongly characterized by implicit user interaction, more recently, automation has been adopted also for the provision of interactive and immersive experiences that actively involve the users. IoT technology thus becomes the key for Smart Interactive Experiences (SIEs), i.e., immersive automated experiences created by orchestrating different devices to enable smart environments to fluidly react to the final users’ behavior. There are domains, e.g., cultural heritage, where these systems and the SIEs can support and provide several benefits. However, experts of such domains, while intrigued by the opportunity to induce SIEs, are facing tough challenges in their everyday work activities when they are required to automate and orchestrate IoT devices without the necessary coding skills. This paper presents a design approach that tries to overcome these difficulties thanks to the adoption of ontologies for defining Event-Condition-Action rules. More specifically, the approach enables domain experts to identify and specify properties of IoT devices through a user-defined semantics that, being closer to the domain experts’ background, facilitates them in automating the IoT devices behavior. We also present a study comparing three different interaction paradigms conceived to support the specification of user-defined semantics through a “transparent” use of ontologies. Based on the results of this study, we work out some lessons learned on how the proposed paradigms help domain experts express their semantics, which in turn facilitates the creation of interactive applications enabling SIEs.

scholarly journals Robotic experiments with cooperative Aerobots and underwater swarms

Robotica ◽  
2009 ◽  
Vol 27 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Ehsan Honary ◽  
Frank McQuade ◽  
Roger Ward ◽  
Ian Woodrow ◽  
Andy Shaw ◽  
...  
Keyword(s):  
Computer Simulations ◽  
Real World ◽  
European Space Agency ◽  
Underwater Vehicles ◽  
Lessons Learned ◽  
Data Handling ◽  
The Real ◽  
Unmanned Underwater Vehicles ◽  
Space Agency ◽  
Processing Power

SUMMARYSciSys has been involved in the development of Planetary Aerobots (arial robots) funded by the European Space Agency for use on Mars and has developed image-based localisation technology as part of the activity. However, it is possible to use Aerobots in a different environment to investigate issues regarding robotics behaviour, such as data handling, limited processing power, and limited sensors. This paper summarises the activity where an Aerobot platform was used to investigate the use of multiple autonomous unmanned underwater vehicles (UUVs) by simulating their movement and behaviour. It reports on the computer simulations and the real-world tests carried out and the lessons learned from these experiments.

scholarly journals DIRECT SIMULATIONS OF SMALL MULTI-FERMION SYSTEMS

2003 ◽  
Vol 14 (08) ◽  
pp. 1027-1040
Author(s):  
MICHAEL CREUTZ
Keyword(s):  
Renormalization Group ◽  
Computer Simulations ◽  
Large Volume ◽  
Lattice Systems ◽  
Small Systems ◽  
Natural Mapping ◽  
Fermion Systems ◽  
Occupation Numbers ◽  
Computer Resources ◽  
System Volume

I explore computer simulations of the dynamics of small multi-fermion lattice systems. The method is more general, but I concentrate on Hubbard type models where the fermions hop between a small number of connected sites. I use the natural mapping of fermion occupation numbers onto computer bits. Signs from fermion interchange are reduced to bit counting. The technique inherently requires computer resources growing exponentially with the system volume; so, it restricted to modestly small systems. Large volume results would require combining these techniques with further approximations, perhaps in a recursive renormalization group manner.

scholarly journals Partly Cloudy with a Chance of Migration: Weather, Radars, and Aeroecology

2012 ◽  
Vol 93 (5) ◽  
pp. 669-686 ◽  
Author(s):  
Phillip B. Chilson ◽  
Winifred F. Frick ◽  
Jeffrey F. Kelly ◽  
Kenneth W. Howard ◽  
Ronald P. Larkin ◽  
...  
Keyword(s):  
Earth Science ◽  
Weather Conditions ◽  
Scientific Discipline ◽  
Biological Research ◽  
Free Atmosphere ◽  
Spatial And Temporal Scales ◽  
Weather Radars ◽  
Radar Systems ◽  
Wide Range ◽  
Patterns And Processes

Aeroecology is an emerging scientific discipline that integrates atmospheric science, Earth science, geography, ecology, computer science, computational biology, and engineering to further the understanding of biological patterns and processes. The unifying concept underlying this new transdisciplinary field of study is a focus on the planetary boundary layer and lower free atmosphere (i.e., the aerosphere), and the diversity of airborne organisms that inhabit and depend on the aerosphere for their existence. Here, we focus on the role of radars and radar networks in aeroecological studies. Radar systems scanning the atmosphere are primarily used to monitor weather conditions and track the location and movements of aircraft. However, radar echoes regularly contain signals from other sources, such as airborne birds, bats, and arthropods. We briefly discuss how radar observations can be and have been used to study a variety of airborne organisms and examine some of the many potential benefits likely to arise from radar aeroecology for meteorological and biological research over a wide range of spatial and temporal scales. Radar systems are becoming increasingly sophisticated with the advent of innovative signal processing and dual-polarimetric capabilities. These capabilities should be better harnessed to promote both meteorological and aeroecological research and to explore the interface between these two broad disciplines. We strongly encourage close collaboration among meteorologists, radar scientists, biologists, and others toward developing radar products that will contribute to a better understanding of airborne fauna.

scholarly journals Preparing Scholarly Practitioners: Redesigning the EdD to Reflect CPED Principles

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Deborah S. Peterson
Keyword(s):  
Design Process ◽  
Practical Wisdom ◽  
Lessons Learned ◽  
Education Administration ◽  
Colleges Of Education ◽  
State University ◽  
Implementation Challenges ◽  
Complex Organization ◽  
Portland State University ◽  
Problems Of Practice

CPED presents guiding principles, rather than a prescriptive program model, for the EdD, requiring each CPED-influenced institution to engage in a program design process specific to its context. Over 80 CPED schools and colleges of education offer an EdD program that endorses the CPED framework which “blend[s] practical wisdom with professional skills and knowledge to name, frame, and solve problems of practice…”(CPED, 2010). As with any design process in a complex organization, faculty members may wonder where to begin. This article describes the context, guiding values, characteristics of our redesigned EdD, lessons learned, and implementation challenges of the education administration faculty in the Graduate School of Education at Portland State University as we increased our focus on CPED principle #1, a focus on “equity, ethics, and social justice to bring about solutions to complex problems of practice” (CPED, 2009). 

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