Bio-Logic Builder: A Non-Technical Tool for Building Dynamical,Qualitative Models

Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized “bio-logic” modules have been defined to provide users with the building blocks for many biological processes. To build/modify computational models, experimentalists provide purely qualitative information about a particular regulatory mechanisms as is generally found in the laboratory. The Bio-Logic Builder subsequently converts the provided information into a mathematical representation described with Boolean expressions/rules. We used this tool to build a number of dynamical models, including a 130-protein large-scale model of signal transduction with over 800 interactions, influenza A replication cycle with 127 species and 200+ interactions, and mammalian and budding yeast cell cycles. We also show that any and all qualitative regulatory mechanisms can be built using this tool.     

Cup plant,an alternative to conventional silage from a LCA perspective

Purpose

The growing awareness of the importance of biodiversity in agroecosystems in increasing and ensuring the supply of biomass has led to heightened interest from governments and farmers in alternative crops. This article assesses one such alternative crop, cup plant (Silphium perfoliatum L.), in terms of the environmental aspects of cultivation for forage production. Many studies have previously focused on cup plant, but so far, this plant has not been assessed using the life cycle assessment (LCA) method.

Materials and methods

This study compares the environmental load of cup plant with the most commonly grown silage crops in Central European conditions—maize—and with another common forage crop—lucerne using LCA. The system boundaries include all the processes from cradle to farm gate and both mass-based (1 ton of dry matter) and area-based (1 ha of monoculture) functional units were chosen for the purposes of this study. The results cover the impact categories related to the agricultural LCAs, and the ReCiPe Midpoint (H) characterization model was used for the data expression, by using SimaPro 9.0.0.40 software.

Results

This study compares the cultivation of cup plant with the most commonly grown silage crop in Central European conditions—maize—and with another common forage crop—lucerne. The paper shows the potential of cup plant to replace conventional silage (maize and lucerne silage mix) with certain environmental savings in selected impact categories, and importantly, while still maintaining the same performance levels in dairy farming as with conventional silage, as already reported in previous publications. For the Czech Republic alone, this would, in practice, mean replacing up to 50,000 ha of silage maize and reducing the environmental load by about tens of percent or more within the various impact categories and years of cultivation.

Conclusion

Cup plant can replace the yield and quality of silage maize, represents a lower environmental load per unit of production and unit of area and generally carries many other benefits. Thus, cup plant is a recommendable option for dairy farming. Given the recent experience and knowledge of the issue, the cup plant can be considered an effective alternative to conventional silage.