GLBRC Research Tools
On our research tools page, you can find a selection of web-based research tools and applications, developed collaboratively between GLBRC scientists and our Information Services (IS) group. If you are looking for a different tool or have any questions, contact IS Coordinator Dirk Norman (dirk.norman@wisc.edu).
Biomass Utilization Superstructure (BUS)
Biomass Utilization Superstructure (BUS) is an online tool for the evaluation of new and existing biofuels strategies. Users can modify and generate a new technology network that consists of a wide range of conversion technologies along with the corresponding feedstocks, intermediates, and final products.
COnTORT: COmprehensive Transcriptomic Organization Tool
COnTORT is a publicly available Python3 program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream bioinformatic applications.
CRISpy-pop
CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing. This tool focuses on generating guide RNA sequences for yeast and bacterial species used in bioenergy research. This tool supports a 1011 genome Saccharomyces cerevisiae strain set as well as a 167 strain set of S. cerevisiae isolates.
Delila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding Motifs
Predicting potential DNA binding motifs is a critical part of understanding gene expression across all domains of life. Here, we report the development of Delila-PY, an easy-to-use pipeline for utilizing the Delila suite of software to identify DNA binding motifs. The Delila-PY Docker image can be found on the Docker hub.
Genomic expression and Sequence analysis (GxSeq)
GxSeq is a repository of genomic sequence, annotations, and sample data. Using this site you can interact with genomic data. There are listings of sequence and features that you can search and download, a browser to view genomic data, dynamic tables of expression data and tools to investigate that data.
Growth Curve Analysis Tool (GCAT)
The Growth Curve Analysis Tool is a web-based tool for summarizing microbial growth curves using mathematical modeling. The user interface requires no programming and calls on an R package of the same name which processes input data files, models the curves, calculates important growth parameters from the fits, and returns both graphical and tabular output.
NMR Database of Lignin and Cell Wall Model Compounds
This database was designed to provide a coherent, single source of NMR data of lignin and other plant cell wall model compounds. The database exists in two different formats: a FileMaker Pro database for cross-platform use and an Adobe pdf cross-platform file for viewing and printing. This is the latest public version of the Database, version 2009.
PlantFAdb: a resource for exploring hundreds of plant fatty acid structures synthesized by thousands of plants and their phylogenetic relationships
Over 450 structurally distinct fatty acids are synthesized by plants. We have developed PlantFAdb.org, an internet-based database that allows users to search and display fatty acid composition data for over 9000 plants. PlantFAdb includes more than 17 000 data tables from >3000 publications and hundreds of unpublished analyses.
sppIDer
Yeast 1000 Plus (Y1000+)
The Y1000+ project is funded by the National Science Foundation to determine "The Making of Biodiversity Across the Yeast Subphylum." Over the next five years, the team behind the project will sequence and analyze the genomes of all known yeast species from the subphylum Saccharomycotina to study the evolution of their diverse metabolic and ecological functions.
