Skip to main content

Facilitating Fusarium Oxysporum Computational Research

Project Information

data handling, data wrangling, slurm, debugging, containers, desktops
Project Status: In Progress
Project Region: Northeast
Submitted By: John Griffin
Project Email: jgriffin@umass.edu
Project Institution: UMass Amherst / MGHPCC
Anchor Institution: NE-MGHPCC

Mentors: John Griffin
Students: Brandon Cross

Project Description

Li-Jun Ma at UMass Amherst uses high-throughput sequencing that relies on HPC. We have been adapting her PacBIO SMRTAnalysis pipelines to run in a cluster environment. We are working extensively with PacBIO vendor support, and with the Ask.CI and XSEDE Campus Champions communities to tackle this project. Ask.CI has proved very useful and allowed us to progress farther with one of the pieces of software for Li-jun.

---

Li-Jun Ma, Associate Professor of Biology at UMass Amherst, is researching Fusarium oxysporum. This fungus causes wilt in over 100 plant species including tomato, cotton, watermelon and banana, costing farmers billions of dollars in losses worldwide each year. The disease is difficult to control. Once the soil is infected, the fungus can remain viable for 30 or 40 years, and at present there really is no way to control it. By advancing understanding of the molecular mechanism of fungal pathogenesis, she hopes to increase ways to develop disease-resistant crops.

Dr. Ma uses high-throughput sequencing that relies on HPC. We have been adapting her PacBIO SMRTAnalysis pipelines to run in a cluster environment. We are working extensively with PacBIO vendor support, and with the Ask.CI and XSEDE Campus Champions communities to tackle this project. Ask.CI has proved very useful and allowed us to progress farther with one of the pieces of software for Li-jun.

This work is supported by an NSF CAREER grant. Ma is also supported by a Burroughs Wellcome Fund award to understand pathogenesis and develop new treatment options for human infections caused by fungal pathogens in the same species.

Project Information

data handling, data wrangling, slurm, debugging, containers, desktops
Project Status: In Progress
Project Region: Northeast
Submitted By: John Griffin
Project Email: jgriffin@umass.edu
Project Institution: UMass Amherst / MGHPCC
Anchor Institution: NE-MGHPCC

Mentors: John Griffin
Students: Brandon Cross

Project Description

Li-Jun Ma at UMass Amherst uses high-throughput sequencing that relies on HPC. We have been adapting her PacBIO SMRTAnalysis pipelines to run in a cluster environment. We are working extensively with PacBIO vendor support, and with the Ask.CI and XSEDE Campus Champions communities to tackle this project. Ask.CI has proved very useful and allowed us to progress farther with one of the pieces of software for Li-jun.

---

Li-Jun Ma, Associate Professor of Biology at UMass Amherst, is researching Fusarium oxysporum. This fungus causes wilt in over 100 plant species including tomato, cotton, watermelon and banana, costing farmers billions of dollars in losses worldwide each year. The disease is difficult to control. Once the soil is infected, the fungus can remain viable for 30 or 40 years, and at present there really is no way to control it. By advancing understanding of the molecular mechanism of fungal pathogenesis, she hopes to increase ways to develop disease-resistant crops.

Dr. Ma uses high-throughput sequencing that relies on HPC. We have been adapting her PacBIO SMRTAnalysis pipelines to run in a cluster environment. We are working extensively with PacBIO vendor support, and with the Ask.CI and XSEDE Campus Champions communities to tackle this project. Ask.CI has proved very useful and allowed us to progress farther with one of the pieces of software for Li-jun.

This work is supported by an NSF CAREER grant. Ma is also supported by a Burroughs Wellcome Fund award to understand pathogenesis and develop new treatment options for human infections caused by fungal pathogens in the same species.