SMART: Spatial Modeling Algorithms for Reaction and Transport

Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of intracellular subcompartments such as membrane-bound organelles. These geometries are now compatible with predictive modeling of cellular function. Biological cells respond to stimuli through sequences of chemical reactions generally referred to as cell signaling pathways. The propagation and reaction of chemical substances in cell signaling pathways can be represented by coupled nonlinear systems of reaction-transport equations. These reaction pathways include numerous chemical species that react across boundaries or interfaces (e.g., the cell membrane and membranes of organelles within the cell) and domains (e.g., the bulk cell volume and the interior of organelles). Such systems of multi-dimensional partial differential equations (PDEs) are notoriously difficult to solve because of their high dimensionality, non-linearities, strong coupling, stiffness, and potential instabilities. In this work, we describe Spatial Modeling Algorithms for Reactions and Transport (SMART), a high-performance finite-element-based simulation package for model specification and numerical simulation of spatially-varying reaction-transport processes. SMART is based on the FEniCS finite element library, provides a symbolic representation framework for specifying reaction pathways, and supports geometries in 2D and 3D including large and irregular cell geometries obtained from modern ultrastructural characterization methods.Comment: 5 pages, 2 figures, submitted to the Journal of Open Source Software (JOSS), code available at https://github.com/RangamaniLabUCSD/smar

Semi-automatic assessment of unrestrained Java code: a Library, a DSL, and a workbench to assess exams and exercises

© ACM 2015. This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in http://dx.doi.org/10.1145/2729094.2742615Automated marking of multiple-choice exams is of great interest in university courses with a large number of students. For this reason, it has been systematically implanted in almost all universities. Automatic assessment of source code is however less extended. There are several reasons for that. One reason is that almost all existing systems are based on output comparison with a gold standard. If the output is the expected, the code is correct. Otherwise, it is reported as wrong, even if there is only one typo in the code. Moreover, why it is wrong remains a mystery. In general, assessment tools treat the code as a black box, and they only assess the externally observable behavior. In this work we introduce a new code assessment method that also verifies properties of the code, thus allowing to mark the code even if it is only partially correct. We also report about the use of this system in a real university context, showing that the system automatically assesses around 50% of the work.This work has been partially supported by the EU (FEDER) and the Spanish Ministerio de Economíay Competitividad (Secretaría de Estado de Investigación, Desarrollo e Innovación) under grant TIN2013-44742-C4-1-R and by the Generalitat Valenciana under grant PROMETEOII2015/013. David Insa was partially supported by the Spanish Ministerio de Educación under FPU grant AP2010-4415.Insa Cabrera, D.; Silva, J. (2015). Semi-automatic assessment of unrestrained Java code: a Library, a DSL, and a workbench to assess exams and exercises. ACM. https://doi.org/10.1145/2729094.2742615SK. A Rahman and M. Jan Nordin. A review on the static analysis approach in the automated programming assessment systems. In National Conference on Programming 07, 2007.K. Ala-Mutka. A survey of automated assessment approaches for programming assignments. In Computer Science Education, volume 15, pages 83--102, 2005.C. Beierle, M. Kula, and M. Widera. Automatic analysis of programming assignments. In Proc. der 1. E-Learning Fachtagung Informatik (DeLFI '03), volume P-37, pages 144--153, 2003.J. Biggs and C. Tang. Teaching for Quality Learning at University : What the Student Does (3rd Edition). In Open University Press, 2007.P. Denny, A. Luxton-Reilly, E. Tempero, and J. Hendrickx. CodeWrite: Supporting student-driven practice of java. In Proceedings of the 42nd ACM technical symposium on Computer science education, pages 09--12, 2011.R. Hendriks. Automatic exam correction. 2012.P. Ihantola, T. Ahoniemi, V. Karavirta, and O. Seppala. Review of recent systems for automatic assessment of programming assignments. In Proceedings of the 10th Koli Calling International Conference on Computing Education Research, pages 86--93, 2010.H. Kitaya and U. Inoue. An online automated scoring system for Java programming assignments. In International Journal of Information and Education Technology, volume 6, pages 275--279, 2014.M.-J. Laakso, T. Salakoski, A. Korhonen, and L. Malmi. Automatic assessment of exercises for algorithms and data structures - a case study with TRAKLA2. In Proceedings of Kolin Kolistelut/Koli Calling - Fourth Finnish/Baltic Sea Conference on Computer Science Education, pages 28--36, 2004.Y. Liang, Q. Liu, J. Xu, and D. Wang. The recent development of automated programming assessment. In Computational Intelligence and Software Engineering, pages 1--5, 2009.K. A. Naudé, J. H. Greyling, and D. Vogts. Marking student programs using graph similarity. In Computers & Education, volume 54, pages 545--561, 2010.A. Pears, S. Seidman, C. Eney, P. Kinnunen, and L. Malmi. Constructing a core literature for computing education research. In SIGCSE Bulletin, volume 37, pages 152--161, 2005.F. Prados, I. Boada, J. Soler, and J. Poch. Automatic generation and correction of technical exercices. In International Conference on Engineering and Computer Education (ICECE 2005), 2005.M. Supic, K. Brkic, T. Hrkac, Z. Mihajlovic, and Z. Kalafatic. Automatic recognition of handwritten corrections for multiple-choice exam answer sheets. In Information and Communication Technology, Electronics and Microelectronics (MIPRO), pages 1136--1141, 2014.S. Tung, T. Lin, and Y. Lin. An exercise management system for teaching programming. In Journal of Software, 2013.T. Wang, X. Su, Y. Wang, and P. Ma. Semantic similarity-based grading of student programs. In Information and Software Technology, volume 49, pages 99--107, 2007

Research Agenda for Studying Open Source II: View Through the Lens of Referent Discipline Theories

In a companion paper [Niederman et al., 2006] we presented a multi-level research agenda for studying information systems using open source software. This paper examines open source in terms of MIS and referent discipline theories that are the base needed for rigorous study of the research agenda

Myths and Realities about Online Forums in Open Source Software Development: An Empirical Study

The use of free and open source software (OSS) is gaining momentum due to the ever increasing availability and use of the Internet. Organizations are also now adopting open source software, despite some reservations, in particular regarding the provision and availability of support. Some of the biggest concerns about free and open source software are post release software defects and their rectification, management of dynamic requirements and support to the users. A common belief is that there is no appropriate support available for this class of software. A contradictory argument is that due to the active involvement of Internet users in online forums, there is in fact a large resource available that communicates and manages the provision of support. The research model of this empirical investigation examines the evidence available to assess whether this commonly held belief is based on facts given the current developments in OSS or simply a myth, which has developed around OSS development. We analyzed a dataset consisting of 1880 open source software projects covering a broad range of categories in this investigation. The results show that online forums play a significant role in managing software defects, implementation of new requirements and providing support to the users in open source software and have become a major source of assistance in maintenance of the open source projects

A Research Agenda for Studying Open Source I: A Multi-Level Framework

This paper presents a research agenda for studying information systems using open source software A multi-level research model is developed at five discrete levels of analysis: (1) the artifact; (2) the individual; (3) the team, project, and community; (4) the organization; and (5) society. Each level is discussed in terms of key issues within the level. Examples are based on prior research. In a companion paper, [Niederman, et al 2006], we view the agenda through the lens of referent discipline theories

A Study on the Open Source Digital Library Software's: Special Reference to DSpace, EPrints and Greenstone

The richness in knowledge has changed access methods for all stake holders in retrieving key knowledge and relevant information. This paper presents a study of three open source digital library management software used to assimilate and disseminate information to world audience. The methodology followed involves online survey and study of related software documentation and associated technical manuals.Comment: 9 Pages, 3 Figures, 1 Table, "Published with International Journal of Computer Applications (IJCA)