Systems Biology Graphical Notation: Process Description language Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

Systems Biology Graphical Notation: Process Diagram Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

Systems Biology Graphical Notation: Process Description language Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

Teaching and learning secondary school biology with diagrams

This thesis comprises a series of inter-related studies that examined: (1) diagrams presented in commonly used biology textbooks in Western Australian schools; (2) teachers’ use of diagrams as part of their normal teaching routines; (3) students’ perceptions of how they learn about diagrams in their lessons; and (4) students’ use of text and diagrams in explaining two phenomena in biology that had not been presented in class.Phase one of the research reports the results of an analysis diagrams presented in biology textbooks used by Western Australian students to examine their distribution pattern. Three types of diagrams (iconic, schematic, and charts & graphs) were investigated in science education based on the work of Novick (2006). Therefore, content analysis in this research entailed a systematic reading and categorizing of these diagrams from a number of secondary school textbooks. The textbook types include lower secondary general science textbooks, upper secondary biology textbooks, and biology workbooks. Descriptive statistics were conducted in order to provide first-hand data on exploring how diagrams are used in biology books. Findings of the study suggest that the three types of diagrams are distributed with unique patterns in the secondary biology textbooks.Phase two reports the investigation of biology teachers’ use of diagrams in their classroom teaching. Biology teachers’ teaching was observed in order to determine instructional methods related to diagrammatic teaching and learning in the natural environment. This study described and analysed how teachers of biology use the three different types of diagrams to introduce, explain and evaluate abstract biology concepts.The third phase of the research reports an analysis of how students think about their teachers’ instructional strategies when teaching with diagrams. An instrument was developed from a previously existing instrument to help students reflect upon their use of diagrams during their teachers’ instruction. The questionnaire data indicated that most participant students recognised teachers’ instructional methods in teaching diagrammatic representations as being explanatory tools, in representing biological concepts, and in help assessing their learning. The three dimensions identified by the questionnaire (Instruction with diagram, Assessment with diagrams and Student diagrammatic competence), demonstrated that students’ perceived experienced biology teachers as being more skillful in having diagrams to engage their learning.Phase four investigated students’ conceptual learning of diagrams alongside other modes of representations. The purpose of this phase was to determine how the students interpreted diagrams together with their counterpart – text – when learning three different biology concepts using an interview protocol. In each interview, students were presented with a biological concept with diagrammatic representation (iconic, schematic diagrams, and charts & graphs) together with textual representation (such as written text and chemical equations). The chapter concludes by showing that diagram and text serve different functional roles in students’ conceptual learning when one or both representations are presented. The results showed that diagram and text may constrain, construct or complementary each other so as to help students understand the complex concept.The final chapter draws together and discusses the findings generated in all of the previous studies in which diagrams were used in various aspects of secondary biological education, such as textbooks, classroom instruction, students’ perceptions, and representational learning with text. The limitations of the research are discussed and suggestions made for future research on the instructional usage of diagrams in biological teaching and learning

The Development of an Instrument for Assessing Students' Perceptions of Biology Teachers' Instructional Use of Diagrams

Science teaching involves using scientific diagrams to explain important concepts, to provide visual images, or to motivate students. However, teachers often wonder if their use of diagrams is effective in helping students learn science. This study aimed to help science teachers evaluate how students perceive their use of diagrams during instruction. Subsequently, we adapted an instrument to measure students' perceptions of science teachers' instructional use of diagrams based on Tuan et al.'s (2000) Student Perceptions of Teachers' Knowledge (SPOTK) questionnaire. The adapted instrument initially had four categories - teacher's instructional practice in using diagrams; teacher's use of multiple forms of scientific representations; teacher's use of diagrams in assessment practices; and students' understanding of and competence in using scientific diagrams. The instrument was administered to 215 Australian high school biology students in Years 9-10. Following factor analysis, 20 items remained in the final instrument and three scales were extracted - Instruction with Diagrams, Assessment with Diagrams, and Students' Diagrammatic Competency. The reliability of the total instrument Students' Perceptions of Teachers' Use of Biology Diagrams was 0.91 and the reliability of each category ranged from 0.65 to 0.90. This instrument is specifically related to the diagrammatic usage in biology lessons and, hopefully, with further research can be generalised to other science lessons. Future research will investigate the relationship between teachers' instruction with diagrams and students' understanding of them

Reverse-engineering of polynomial dynamical systems

Multivariate polynomial dynamical systems over finite fields have been studied in several contexts, including engineering and mathematical biology. An important problem is to construct models of such systems from a partial specification of dynamic properties, e.g., from a collection of state transition measurements. Here, we consider static models, which are directed graphs that represent the causal relationships between system variables, so-called wiring diagrams. This paper contains an algorithm which computes all possible minimal wiring diagrams for a given set of state transition measurements. The paper also contains several statistical measures for model selection. The algorithm uses primary decomposition of monomial ideals as the principal tool. An application to the reverse-engineering of a gene regulatory network is included. The algorithm and the statistical measures are implemented in Macaulay2 and are available from the authors

Students’ ability to solve process-diagram problems in secondary biology education

Process diagrams are important tools in biology for explaining processes such as protein synthesis, compound cycles and the like. The aim of the present study was to measure the ability to solve process-diagram problems in biology and its relationship with prior knowledge, spatial ability and working memory. For this purpose, we developed a test that represents process diagrams and adjacent tasks used in secondary education biology. Results show that the ability to solve process-diagram problems is correlated to prior knowledge, spatial abilities and visuospatial working memory capacity. A difference in impact of spatial skills was demonstrated for the level of cognitive demand when solving process-diagram problems

VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams.

BackgroundVisualization of data generated by high-throughput, high-dimensionality experiments is rapidly becoming a rate-limiting step in computational biology. There is an ongoing need to quickly develop high-quality visualizations that can be easily customized or incorporated into automated pipelines. This often requires an interface for manual plot modification, rapid cycles of tweaking visualization parameters, and the generation of graphics code. To facilitate this process for the generation of highly-customizable, high-resolution Venn and Euler diagrams, we introduce VennDiagramWeb: a web application for the widely used VennDiagram R package. VennDiagramWeb is hosted at http://venndiagram.res.oicr.on.ca/ .ResultsVennDiagramWeb allows real-time modification of Venn and Euler diagrams, with parameter setting through a web interface and immediate visualization of results. It allows customization of essentially all aspects of figures, but also supports integration into computational pipelines via download of R code. Users can upload data and download figures in a range of formats, and there is exhaustive support documentation.ConclusionsVennDiagramWeb allows the easy creation of Venn and Euler diagrams for computational biologists, and indeed many other fields. Its ability to support real-time graphics changes that are linked to downloadable code that can be integrated into automated pipelines will greatly facilitate the improved visualization of complex datasets. For application support please contact [email protected]

Indispensability and Effectiveness of Diagrams in Molecular Biology

In this paper I aim to defend a twofold thesis. On one hand, I will support, against Perini (2005), the indispensability of diagrams when structurally complex biomolecules are concerned, since it is not possible to satisfactorily use linguistic-sentential representations at that domain. On the other hand, even when diagrams are dispensable I will defend than they will generally be more effective than other representations in encoding biomolecular knowledge, relying on Kulvicki-Shimojima?s diagrammatic effectiveness thesis. Finally, I will ground many epistemic virtues of biomolecular diagrams (understandability, explanatory power, prediction and hypothesis evaluation) on their cognitive-computational indispensability and their semantic-epistemic effectiveness. Keywords: Molecular Biology, Diagrammatic Representation, Representational Indispensability