Research Resources

Collaborative Projects

Boyce Thompson Institute faculty and researchers are involved in a number of projects developing web-based databases to store and organize information related to plant science. Use the following links to explore these collaborations and their resources.

Nicotiana benthamiana

Scientists from BTI and several other institutions are collaborating on a project to improve the genome sequence of Nicotiana benthamiana and develop software tools for its analysis. As part of this effort, a website has been developed that serves as a portal for bioinformatics and experimental resources for this plant species. The website provides various bioinformatics resources including a link for accessing the draft genome sequence of N. benthamiana which was published in 2012.

The draft genome sequence for Nicotiana benthamiana was published by MPMI in 2012.

Sol Genomics Network

sol genomics phenotypesMueller Lab coordinates the Sol Genomics Network, a site for genome data of Solanaceae species such as tomato, potato, and pepper, and related to the tomato genome sequencing project.

CassavaBase

Jeremy Edwards and Lukas Mueller, Uganda

BTI scientists Jeremy Edwards and Lukas Mueller in Africa, May 2014, to meet with plant scientists and bioinformatics specialists.

The Mueller Lab at Boyce Thompson Institute for Plant Research (BTI) coordinates CassavaBase, a website where scientists who are working to improve cassava breeding can share data and resources. This effort is part of NextGen Cassava, a project supported by the Bill and Melinda Gates Foundation.

Additional Databases and Tools

Use the following links to explore many more databases and online tools generated and curated at BTI:

Tomato Expression Atlas
A high resolution map and search tool for tomato genes and their products.

SGN VIGS Tool
User-friendly software to design virus-induced gene silencing (VIGS) constructs for functional genomics.

Tomato Functional Genomics Database
A genomic and genetic database for the tomato.

Tomato Epigenome Database
A web-based database that allows user to get information related to epigenomic data, such us DNA methylation data, combined with visualization tool Generic Genome browser.

Cucurbit Genomics Database
A tool for the cucurbit research community; a genomic and genetic database for different types of melon.

Kiwifruit Genome Database
Pre-publication kiwifruit genome sequences and annotations for use by public and private research communities as a resource to facilitate plant biology discoveries and plant breeding programs.

RadishBase
A genomic and genetic database for the radish.

MusaBase
A breeding database designed for advanced breeding methods in banana breeding.

SweetPotatoBase

YamBase

Software

Boyce Thompson Institute (BTI) faculty and researchers use many different types of software tools to accomplish a great deal of their biological analyses. Use the following links to explore the different software tools further.

iAssembler
A standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs.

iTAK
A program to identify plant transcription factors (TFs), transcriptional regulators (TRs), and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs, and PKs into different gene families.

Plant MetGenMAP
A visualization and analysis package that allows you to identify changed pathways and enriched GO terms from gene expression and/or metabolite profile data and to visualize the profile data in a biochemical pathway context.

For information on BTI’s bioinformatics resources please contact Dr. Lukas Mueller to arrange for server space and contact Dr. Suzy Strickler for bioinformatics consulting.

Equipment Manuals

ÄKTA™ FPLC Chromatography System

Installation Manual (PDF; 1.6 MB)
Making Your First Run (PDF; 1.6 MB)
FPLC_Optional_Config (PDF; 3.4 MB)
System Manual (PDF; 2.4 MB)

Imagers/Scanners

Kodak Image Station 440CF Manual (PDF; 4.6 MB)
Microtek ScanMaker 5950 Manual (PDF; 1.5 MB)
Storm User Manual (PDF; 1.2 MB)
GelDoc XR UV Imaging Quick Guide GK 7.07 2 (PDF; 34 KB)
GelDox_SR_System_Manual (PDF; 2.5 MB)
Nikon_D80_Cameral_manual (PDF; 8.9 MB)

Liquid Scintillation

Beckman LSC LS6500 Manual (PDF; 5.5 MB)

Microplate Readers

SPECTRAmax® PLUS384 User Manual (PDF; 623.1 KB)
SPECTRAmax® PLUS384 User Manual (PDF; 6 MB)

Microscopes

Olympus SZX Base Manual (PDF; 3.4 MB)
Olympus SZX Microscope (PDF; 4.6 MB)

Light Sources

Halogen Light Source Manual (PDF; 538 KB)

Cameras

Olympus MagnaFire Manual (PDF; 2.1 MB)
Optronics MagnaFire Manual (PDF; 2.7 MB)

Refractometers

ABBE-3L Refractometer Manual (PDF; 7.3 MB)

Sequencers

ABI Prism® 3100 Genetic Analyzer Manual (PDF; 3.9 MB)