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CRC News September 2021
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Inside
  • CRC/Pitt IT strategic collaboration
  • CRC collaborators awarded $1.18 million NSF grant for nodes at CRC
  • CRC now covers Matlab license
 
  • COMSOL platform now available
  • Ask Leo: How can I find a specific code?
  • CRC Fall 2021 online workshops
  • Fall 2021 NGS workshop series
Pitt IT's Adam Hobaugh and CRC veteran Kim Wong foster Strategic Collaboration
Adam Hobaugh and Kim Wong

The Center for Research Computing (CRC) has new permanent leadership. Kim Wong and Adam Hobaugh will co-direct the center, connecting the research computing community with Pitt’s Information Technology unit .Appointed by Senior Vice Chancellor for Research Rob Rutenbar, Wong and Hobaugh, who have served as interim co-directors since November 2020, will work to offer Pitt faculty from all backgrounds resources for incorporating advanced computing and data technology into their work.

“CRC’s new co-director structure embodies Pitt’s commitment to both scientific and technical leadership in research computation,” said Rutenbar. “Together, we leverage Pitt IT’s expertise on systems, the cloud and state of the art networking, which allows us to deliver world-class computing and data services to our full spectrum of partners. Adam brings strong IT leadership, and Kim has great leadership strength in science.”
Read more at: Research and IT Foster Strategic Collaboration | University of Pittsburgh


NSF $1.18M Major Research Instrumentation Award to team led by CRC Collaborator Geoff Hutchison 
A team led by Chemistry associate professor Geoff Hutchison has been awarded a $1.18 million National Science Foundation-Major Research Instrumentation grant to acquire GPU and MPI nodes for the Center for Research Computing. The grant will greatly boost CRC's capabilities, especially in AI and machine learning and GPU-accelerated physics-based simulations.. Co-PIs on the proposal are Chemistry associate professor Lillian Chong, Inanc Senocak, associate professor in Mechanical Engineering & Materials Science, and David Koes, associate professor in Systems and Computational Biology.


 
 

 





Researchers can now submit Matlab jobs directly to the clusters from a laptop without purchasing a research license
CRC users can now install Matlab and run directly from their laptops without needing to purchase an annual research license. CRC pays the license to eliminate access restrictions that allowed only students to use Matlab on CRC without purchasing an annual license. CRC offers the Matlab Parallel Server, a set of Matlab functions that allow users to submit jobs from a Matlab desktop session directly to the HPC clusters, allowing less-experienced users to ramp up their workflow and usage with less interaction with the command line through the allows them to take full advantage of the computing power available on the clusters to solve complex problems while using Matlab on their own computers. For more information see: Matlab Remote Job Submission | crc.pitt.edu | University of Pittsburgh.

COMSOL platform now available on CRC clusters
CRC now offers the COMSOL Multiphysics cross-platform, a finite element analysis, solver and multi-physics simulation software. COMSOL provides an integrated development environment and unified workflow for electrical, mechanical, fluid, acoustics, and chemical applications. With COMSOL, an application programming interface for Java and LiveLink may be used to control the software externally, with an Application Builder to develop custom domain-specific simulation applications. COMSOL allows users to use drag-and-drop tools or command-line programming. Several modules are available for applications in Electrical, Mechanical, Fluid, Acoustic, Chemical, Multipurpose, and Interfacing. For more information see: COMSOL Multiphysics | crc.pitt.edu | University of Pittsburgh.

Ask Leo: How can I find out if a specific code is installed on the CRC cluster?
CRC consultant and research assistant professor Leonardo Bernasconi answers common questions we hear from CRC users.
CRC maintains a list of software packages installed on the cluster, which is available at https://crc.pitt.edu/installed_software. The easiest way to check whether specific software is installed is the “module spider” command, which provides the most up to date information.

For instance, for the “Gaussian" code, the command "module spider gaussian" returns all versions of the code installed and also provides information on how to access the software by loading the corresponding module. If a specific code appears not to be available with the “module spider” command you can request its installation by submitting a ticket at Submit a ticket | crc.pitt.edu | University of Pittsburgh.

CRC Fall 2021 Online Workshops
Register for all workshops at CRC Fall 2021 Online Workshop Registration | crc.pitt.edu | University of Pittsburgh. You will receive an email with a Zoom link and password one week before the workshop.
  • R Programming for Beginners, Thursday, Oct. 7, 1-4pm
    Presented by research associate professor Kim Wong. Hands-on training on the R language syntax, how to run R code on the cluster, and strategies for parallelizing R code. 

     
  • Introduction to ab initio Part 1, Thursday, Oct. 14, 1-4pm
    Introduction to ab initio electronic structure calculations for molecules and extended systems. The mean-field approximation and the Hartree-Fock method. Electronic correlation. Density-functional theory. Excited states: time-dependent density-functional theory. Presented by research assistant professor Leonardo Bernasconi.

     
  • Introduction to ab initio Part 2, Thursday, Oct. 21, 1-4pm
    Ab initio simulation of condensed phases. Crystal structure and symmetry. Band-structure calculations. Software for ab initio calculations in extended systems: plane-waves versus local basis functions. Ab initio molecular dynamics (AIMD): the Car-Parrinello and Born-Oppenheimer methods. AIMD in practice: simulation of chemical reactions in complex environments. Presented by research assistant professor Leonardo Bernasconi.

Fall 2021 Next Generation Sequencing Workshops
Find more information at Fall 2021 Next Generation Sequencing Workshops | crc.pitt.edu | University of Pittsburgh. These workshops were supported in part by the University of Pittsburgh seed project titled "University of Pittsburgh Computational Genomics Training Program."

Differential Expression and Functional Analysis
Tuesday, Oct. 5, 1 - 4pm
This hands-on workshop will introduce participants to statistical methods and considerations used to perform differential gene expression analysis on bulk RNA-seq data using DESEQ2. The workshop will also provide an overview of tools for functional analysis of DE genes to make biological inferences from large gene lists. Presented by Dhivyaa Rajasundaram.
Register at: Fall 2021 NGS Workshops Registration

Introduction to NGS data analysis
Thursday, Oct. 14, 1 - 4pm
High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. This workshop covers common file formats for sequence data and limitations of sequencing technologies. This workshop introduces the more “universal” aspects of high-throughput sequence analysis. We will explore a hands-on exercise focusing on DNAseq data processing. Presented by Riyue Bao.
Register at: Fall 2021 NGS Workshops Registration

ChIP-seq and ATAC-seq data analysis
Tuesday, Oct. 26, 1 - 4pm
This workshop will provide both theoretical and practical introduction to ChIP-seq and ATAC-Seq data analysis. In the first section, we will present the principle of ChIP and ATAC sequencing, bioinformatics pipeline of peak calling, data visualization, method of motif discovery, and a brief introduction of CUT&RUN sequencing. In the second half of the workshop, we will hand on a real ChIP-seq dataset to practice the pipeline using the HTC cluster. Presented by Silvia Liu.
Register at: Fall 2021 NGS Workshops Registration

scRNASeq data analysis using R 
Tuesday, Nov. 2, 1 - 4pm
This workshop will briefly review the cellranger pipelines to process raw reads into expression values. The hands-on training will include reading the count data in R, quality control, normalization, dimensionality reduction, cell clustering, and finding marker genes. The Seurat pipeline will be covered. It also includes the integrative analysis of simulated vs control data using the anchoring framework in Seurat V3. Presented by Dhivyaa Rajasundaram.
Register at: Fall 2021 NGS Workshops Registration

 
WES/WGS variant calling 
Tuesday, Nov. 9, 1 - 4pm
This workshop will provide an overview and hands-on practice for whole exome sequencing (WES) somatic variant calling in tumor tissues. In Part I, we will review key analysis steps, quality evaluation metrics, and statistical algorithms with a focus on the GATK4-MuTect2 best practices. In Part II, we will run somatic variant calling and annotation workflow on real-world WES data via Unix / Linux commands on the HTC cluster. Presented by Silvia Liu
Register at: Fall 2021 NGS Workshops Registration

Amplicon sequencing data analysis
Thursday, Nov. 11, 1 - 4pm
This workshop provides an introduction to the amplicon sequencing analysis from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the amplicon sequencing data beyond QIIME, including statistical analyses and functional analyses. Presented by Riyue Bao
Register at: Fall 2021 NGS Workshops Registration
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