VTechWorks staff will be away for the Thanksgiving holiday beginning at noon on Wednesday, November 27, through Friday, November 29. We will resume normal operations on Monday, December 2. Thank you for your patience.

Browsing by Author "Megraw, Molly"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future
    Doherty, Colleen; Friesner, Joanna; Gregory, Brian; Loraine, Ann; Megraw, Molly; Meyers, Blake C.; Provart, Nicholas J.; Slotkin, R. Keith; Town, Chris; Assmann, Sarah M.; Axtell, Michael J.; Berardini, Tanya; Chen, Sixue; Gehan, Malia; Huala, Eva; Jaiswal, Pankaj; Larson, Stephen; Li, Song; May, Sean; Michael, Todd; Pires, J. Chris; Topp, Chris; Walley, Justin; Wurtele, Eve (Wiley, 2019-01-01)
    Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resources include reference genome sequence data and an ever-increasing number of diverse data sets and data types. TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAIC held another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community-defined common standards for data and metadata, and accessible and user-friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less-established standards (e.g., phenomics, metabolomics). Community-established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a "one-stop shop" website, an Arabidopsis "Super-Portal" to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy-in and participation in its establishment and development to encourage adoption.
  • Thumbnail Image
    PlantSimLab - a modeling and simulation web tool for plant biologists
    Ha, Sook; Dimitrova, ‪Elena; Hoops, Stefan; Altarawy, Doaa; Ansariola, Mitra; Deb, Devdutta; Glazebrook, Jane; Hillmer, Rachel; Shahin, Hossameldin L.; Katagiri, Fumiaki; McDowell, John M.; Megraw, Molly; Setubal, João C.; Tyler, Brett M.; Laubenbacher, Reinhard C. (2019-10-21)
    Background At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling. One of the biggest challenges to making this integration a reality is that many life scientists do not possess the mathematical expertise needed to build and manipulate mathematical models well enough to use them as tools for hypothesis generation. Available modeling software packages often assume some modeling expertise. There is a need for software tools that are easy to use and intuitive for experimentalists. Results This paper introduces PlantSimLab, a web-based application developed to allow plant biologists to construct dynamic mathematical models of molecular networks, interrogate them in a manner similar to what is done in the laboratory, and use them as a tool for biological hypothesis generation. It is designed to be used by experimentalists, without direct assistance from mathematical modelers. Conclusions Mathematical modeling techniques are a useful tool for analyzing complex biological systems, and there is a need for accessible, efficient analysis tools within the biological community. PlantSimLab enables users to build, validate, and use intuitive qualitative dynamic computer models, with a graphical user interface that does not require mathematical modeling expertise. It makes analysis of complex models accessible to a larger community, as it is platform-independent and does not require extensive mathematical expertise.