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iCER is currently looking to add an Information Technology Professional to our team. If you or someone

you know is a potential candidate, we encourage you to apply. Applications must be submitted through

Michigan State University Human Resources. For complete details or to apply, please

visit jobs.msu.edu and search job posting #1926.

Subscribe Share Past Issues Translate

We invite you to attend the fourth annual Cyberinfrastrucutre (CI) Forum, formerly known as CI Days. This

event will be held on October 22, 2015 at the MSU Union Ballroom. This free event features:

Special industry guest speakers

Interactive workshops on a variety of topics

Poster competition with the chance to win cash prizes!

Resource fair featuring resources available to researchers

Networking opportunities/evening social hour

Join us as we celebrate CI on October 22, 2015!

Upcoming Trainings

A complete list of upcoming workshops,

details and registration can be seen at

icer.msu.edu/events.

September 10, 2015

Introduction to HPCC

September 1517, 2015

Software Carpentry

September 2122, 2015

RNASequencing Tools

September 22, 2015

Parallel Computing with MATLAB

September 22, 2015

Analyzing and Visualizing Data withMATLAB

September 24, 2015

Advanced Topics in HPCC

September 29, 2015

Intro to SQL and Relational Databases

October 1, 2015

iCER welcomes you to our open office hour eachMonday and Thursday from 1pm – 2pm toreceive one on one help with computationalbased issues. You can find us in the Biomedicaland Physical Sciences Building in Room 1440ready to help!

October 1, 2015

Genome Mapping and Variant Analysis

October 6, 2015

Introduction to Linux/Unix

October 13, 2015

Introduction to HPCC

Don't miss the excitement of the 4thannual CI Forum on Oct. 22, 2015!

Do you know about an event, opportunity, jobposting, or general news that would be ofinterest in our community? We would love tohear about it! Email us at [email protected] andwe will get the word out. All submissions will beposted at the discretion of the iCERCommunication Coordinator.

Copyright © 2015 Michigan State University, Institute for Cyber-Enabled Research, All rights reserved.

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We invite you to attend the 4th Annual Cyberinfrastructure (CI) Forum. This free event will be held

Thursday, October 22 at the MSU Union Ballroom. The CI Forum will feature:

Special industry guest speakers

Interactive workshops on a variety of topics

Poster competition with a chance to win cash prizes

Resource fair

Networking opportunities/evening social hour

Please register by Monday, October 19.


The new iCER website is live!

Upcoming Trainings

A complete list of upcomingworkshops, details and registration

can be seen athttp://icer.msu.edu/upcoming-

workshops.

October 17-18, 2015Avida Software Carpentry Workshop

October 22, 2015State of Art of Multi-PhysicsComputational Simulation

October 27, 2015Beyond Excel: Enhancing Your Data

Analysis with MATLAB

October 27, 2015Financial Modeling and Economic

Analysis with MATLAB

October 30, 2015Python HPC XSEDE Webinar

Dharanya Sampath announced as new

Director of BiCEP.

Python HPC XSEDE WebinarViewing Session

November 10, 2015Introduction to Linux/Unix

November 11, 2015Intermediate Shell Scripting

November 12, 2015Introduction to HPCC

iCER is currently looking to add a ResearchSpecialist to our team. If you or someone youknow is a potential candidate, we encourage you

to apply. Applications must be submitted through

Michigan State University Human Resources. For

complete details or to apply, please

visit jobs.msu.edu and search job posting

#2048.

CMSE graduate materials is now posted— inparticular, a description of the new PhD

program and how to apply. This can be foundat the CMSE web page, https://cmse.msu.edu .

The PhD program info is athttps://cmse.msu.edu/academics/graduate-

program/phd-in-computational-mathematics-science-and-engineering/

iCER, in partnership with four otherinstitutions, recieved a $5 million

grant from the National Science Foundation to implement

the Multi-Institutional Open StorageResearch InfraStructure (MI-OSiRIS),providing high-speed infrastructure for

scientists to access and share theirresearch across the region with

unprecedented ease. See (link to MSUtoday) for more information.

http://msutoday.msu.edu/news/2015/msu-

nets-part-of-5m-big-data-grant-from-national-science-foundation/

iCER welcomes you to our open office hour eachMonday and Thursday from 1pm – 2pm toreceive one on one help with computationalbased issues. You can find us in the Biomedicaland Physical Sciences Building in Room 1440ready to help!

Special Office HoursOffice hours will be held at a special location onThursday, October 22, 2015 due to the CIForum. You can find our Research Consultants atthe MSU Union, outside the Ballroom from 1-2pm for any questions or help you may need. Wehope to see you there! Regular office hours willresume Monday, October 26, 2015.

Do you know about an event, opportunity, job posting, or general news that would be of interest inour community? We would love to hear about it! Email us at [email protected] and we will get theword out. All submissions will be posted at the discretion of the iCER Communication Coordinator.


iCER represents MSU at SC15This week, the iCER team is attending SC15 in Austin, Texas. We are sharing abooth with University of Michigan, and will be participating in multiple talks andpresentations throughout the conference. This year’s theme is “HPC Transforms,”which we fully endorse and believe in.

Make sure to look for our tweets throughout the week (#icermsu) and check outour Facebook page, as we share many of the events in which MSU will be seenand heard.


our Facebook page, as we share many of the events in which MSU will be seenand heard.

2015 CI Forum a Success

The fourth annual CI Forum, held October 22 at the MSU Union, was aresounding success. Many subjects were covered in the intensive, oneday

event, and more than 100 people attended — more than last year — which is a

promising sign for the iCER program.

Among the highlights:

° Keynote speaker Craig Stewart shared Indiana University’s journey into

becoming a nationallevel HPC research center. Interestingly, several of the

points along IU’s path mirror MSU’s experiences.

° The HPCC team gave two presentations: Current and In-Development HPCC

Computational Resources (Andrew Keen) and Ongoing Developments and

Advances in Future HPCC Technologies (Sharan Kalwani). They talked about

how HPCC is exploring new technologies, and how the team is striving to

become a leader in various areas of expertise, inclue ARMbased and

OpenPOWERbased computing.

° A subject that popped up in several breakout sessions was the growing

importance of Big Data and the HPCC’s preparations to work within these

emerging systems.

° The final keynote talk by Arthur Lupia, which focused on data access and

research transparency, generated a lot of discussion. This kind of interest

bodes well for the kind of audience participation we had hoped for.

Presentations have been posted and shared with the iCER community here.

Outage update

The High Performance ComputingCenter's maintenance window on Nov. 4

was successful. Data stored on theHPCC’s file storage scratch system was

migrated to a new scratch filesystem, andearly tests have shown this new system to

be much faster. Click here for moreinformation, including how this could affect

your old file paths.

HPC Training at iCER This has been an incredible fall for HPCtraining. iCER launched three newworkshops: SQL & Relational Databases,Research Computing at iCER, and GenomeMapping & Variant Analysis. Monthly iCERworkshops attracted more than 200researchers — more than last year — andincluded graduate students (comprising 62percent of attendees) and faculty/post-docs(25 percent).

The basic computational training facilitatedby iCER’s workshops is reaching traditionalscientists at MSU. The majority ofresearchers registered for workshops werefrom the agricultural/biological sciences andnatural resources domains (Fig. 1).

We’ve worked with faculty in both of theseareas to develop and offer tailor-madeworkshops in addition to basic courseofferings.

On Nov. 4, seven members of the iCER staff

volunteered at City Rescue Mission Upscale

Thrift. They spent the morning preparing

merchandise for the floor and distributing

clothing to the racks throughout the store.

Read the full story here.

Upcoming events:

Research Data Management Café

3-5 p.m. Monday, Nov. 23

Main Library, Green Room, Fourth Floor

This event is sponsored by the MSU Clinical and

Translational Sciences Institute (CTSI),

Biomedical Research Informatics Core (BRIC)

and MSU Libraries. This discussion will include:

· Building a data management decision tree

· NIH thinking for data storage and sharing

· Treating data as an acquisition

No registration is necessary. For more

information, click here.

One Hundred Years of Statistical

Developments in Animal Breeding, presented

by guest lecturer Dr. Daniel Gianola

2 p.m. Friday, Dec. 4

Molecular Plant Science Building, Auditorium

Room 1200

Daniel Gianola, the Sewall Wright Professor of

the Department of Animal Sciences and

offerings.

Additionally, training is reaching researchersearly in their careers at MSU. Almost half ofregistrants identify themselves as “between0-1 years” in their current academic role(graduate student, faculty/post doc, etc.) and nearly two-thirds have two years or less(Fig. 2).

Notably, almost half of researchersregistered for iCER workshops were notcurrent HPCC users.

Initial feedback suggests that attendeesvalue these services. Most respondents saidthe workshop they attended effectivelyequipped them with the information theyneeded to conduct research.iCER Research Consultants find that thosewho attend these introductory classes havefewer questions and can get a quicker starton using the HPC for computation in theirresearch (Fig. 3).

Watch for our new “PC to HPC” series nextspring, which is aimed at researchers whowant to gain a practical understanding ofparallel computing concepts. This series of

Department of Dairy Science at the University of

Wisconsin, will talk about the future of big data as

it relates to livestock, plant, and human genomic

projects. Researchers whose fields of expertise

relate to genomics and/or computation will gain

insight from this presentation.

Event details and registration can be found here.

New research video!We recently posted a video highlighting

Dr. Andrew Christlieb's research. Dr.Christlieb studies and models plasma for a

variety of applications, includingprocessing computer chips. You can see

the video here. His research highlights can be seen here.

To further our understanding of MSU'shigh-performance computers, werecently sought the assistance of theCenter for Advanced Microscopy totake a closer look at some of ourcomputer chips. Electron MicroscopistCarol Flegler put some of the HPC’schips and components under the

want to gain a practical understanding ofparallel computing concepts. This series of90-minute talks provides an introduction toparallel computing concepts and algorithmsthrough examples.

Have your say in the workshops iCER offershere.

iCER is currently looking to add an InformationTechnologist to our team. If you or someone you knowis a potential candidate, we encourage you to

apply. Applications must be submitted through Michigan

State University Human Resources.

For complete details or to apply, please

visit jobs.msu.edu and search job posting #1926.

lens of her department’s most powerfulexamination tools. Click here to readthe story.

iCER welcomes you to our open office hour

each Monday and Thursday from 1 p.m. – 2

p.m. to receive one-on-one help with

computational based issues. You can find us in

the Biomedical and Physical Sciences Building in

Room 1440 ready to help!

Special Office HoursThere will be no office hours Thursday-Friday,Nov. 26-27, due to the Thanksgiving holiday.Regular hours will resume Monday, Nov. 30.

Do you know about an event, opportunity, job posting, or general news that would be of interest in our

community? Email us at [email protected] and we will get the word out. All submissions will be posted at the

discretion of the iCER Communications Coordinator.


A Message from the HPCC Director

The annual Supercomputing Conference Series isthe premier event for all things HPC-related. Thisyear’s event in Austin, Texas, called SC15, wasanother highly successful event for MSU’s iCERteam. As we did last year, iCER had a joint boothwith University of Michigan’s Advanced ResearchComputing (ARC) team, which elevated our visibility,and showed the other presenters that even rivals canset aside their differences in the name of science.This year broke the all-time record for attendance,with 12,868 attendees — and a good portion of themvisited us. iCER has gained a lot more visibility, aswas evidenced by the feedback left for us by thevarious visitors. We held six well-receivedpresentations, including one on the long-term planand vision for MSU's research efforts using HPC. We also laid out the major initiatives of our newdepartment, Computational Mathematics, Science and Engineering (CSME). It wasestablished earlier this year to advance the goals of producing trained graduates andconducting research using the new paradigms of computational methods. CMSE isunique among contemporary universities in this regard. MSU is starting to get noticed by the top institutions worldwide for acquiring prowess,skills and capabilities in the HPC arena. Expect to hear more good news in thisregard soon.


-Sharan Kalwani, HPCC Director

Check out the cool time-lapse videoof the construction of iCER's booth

at SC15 by clicking here.

HPC Training at iCER Upcoming Workshops and Seminars Introduction to HPCC

2-4:30 p.m. Wednesday, January 6211 Bessey HallInstructor: Dr. Yongjun Choi Introduction to Python

8:30-11:30 a.m. Thursday, January 7217 Bessey HallInstructor: Sharan Kalwani Introduction to Linux/Unix

9 a.m.-noon Thursday, January 14Biomedical & Physical SciencesBuilding, Room 1455AInstructor: Dr. Xiaoge Wang Introduction to HPCC

9 a.m.-noon Tuesday, January 19Biomedical & Physical SciencesBuilding, Room 1455AInstructor: Patrick Bills Introduction to GIT

11 a.m.-noon Thursday, January 21Location: Biomedical & PhysicalSciences Building, Room 1455AInstructor: Dr. Chun-Min Chang RNA Sequencing Tools

9 a.m.-3 p.m. Monday-Tuesday,January 25-26Biomedical & Physical SciencesBuilding Room 2245

Click here to see our video aboutthis year's successful CI Forum.

Upcoming event: "Faculty Seminars in Research and

Instructional Technology"Wednesday, January 6,

and Thursday, January 7, 2016

Faculty Seminars are two days ofshort courses designed to support

faculty, academic staff, andgraduate assistants in their teaching

and research roles by providinginstruction on a variety of softwaretools. All sessions are held at MSU

in various technology classroomsand computer labs across campus.

Full details, including registrationinformation, can be found here.

We are offering more than 30 half-

day and full-day courses in face-to-face settings. You may choose fromone to four classes over the two-dayperiod, with a free lunch each day at

the MSU Union. All courses areoffered at no charge to faculty and

academic staff.

Building Room 2245Instructor: Dharanya Sampath PC to HPC: Parallel Computing

11:30 a.m.-12:30 p.m.Wednesday, January 27Biomedical & Physical SciencesBuilding, Room 1455AInstructor: Dr. Xiaoge Wang

Click here for registration information.

iCER's on Instragram!

Make sure to follow us, as westart sharing photos and videos of

all the cool stuff we do and the latestHPCC developments.

Outage update Last month, HPCC endured anunforeseen outage in the powerinfrastructure for the compute

equipment. We informed all theusers through every communicationchannel available to us as soon aswe found out, and the entire HPCCteam pitched in and managed theloss of complete power for several

hours.

We successfully accomplished themassive task of restoring the service

back to full levels through carefulplanning and working with our

infrastructure teams on campus. We

Check out the full schedule, and find

expanded course descriptions byclicking here.

The deadline for enrolling in theseFaculty Seminars in Research and

Instructional Technology is Monday,December 28.

New research highlight!We recently posted a research

highlight of Dr. Matthew Scholz'sresearch identifying bacteria by theirgenomes. You can see a summary

of his research here.

iCER welcomes you to our open office

hour each Monday and Thursday from 1–2

p.m. to receive one-on-one help with

computational-based issues.

You can find us in the Biomedical and

Physical Sciences Building in Room 1440

ready to help!

Please note:

There will be no office hours Thursday, Dec. 24 or Thursday, Dec. 31

faced a delay of work gettingcompleted by several hours andthere was a delay in sending out

emails that had gotten batched up,but we’re proud to say that no work

was lost.

We would like to thank our users fortheir understanding and patience. If

you still have issues, please feel freeto contact us.

Regular hours will resume Monday, Jan 4.

Do you know about an event, opportunity, job posting, or general news that would be of interest in

our community? Email us at [email protected] and we will get the word out. Allsubmissions will be posted at the discretion of the iCER Communications Coordinator.



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