Category Archives: Chem-Bio Library

Science Gateways’ presentation & lunch with Dr. Sandra Gesing Oct 30th

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Please join the Data and Computational Science Series (DCSS) team for a (free!) ‘Understanding Science Gateways’ presentation & lunch with Dr. Sandra Gesing, Computational Scientist, University of Notre Dame.

Science Gateways and the Science Gateways Community Institute (SGCI) with Dr. Sandra Gesing

Tuesday October 30 – TUC 400B FREE REGISTRATION

 

 

 

 

 

Science Gateways – also called virtual research environments or virtual labs – allow science and engineering communities to access shared data, software, computing services, instruments and other resources specific to their disciplines and use them also in teaching environments. The U.S. Science Gateways Community Institute (SGCI) provides free resources, services, experts, and ideas for creating and sustaining science gateways.

11am-1pm: General Introduction to Science Gateways & the Science Gateways Community Institute (SGCI) – Lunch provided

1pm-3pm: Science Gateways Presentation On Usability With Hands-On Portion – please bring a laptop

These events are free and open to all.

FREE REGISTRATION

Flyer – DCS2 _Intro to Science Gateways_30oct18

Flyer – DCS2 _Science Gateways Usability presentation_30oct18

General Introduction to Science Gateways & the Science Gateways Community Institute (SGCI)
In the last decade mature complete science gateway frameworks have evolved such as HUBzero, Galaxy, Agave and Apache Airavata. Successful implementations have been adapted for several science gateways, for example, the technologies behind the science gateways CIPRES, which is used by over 25.000 users to date and serves the community in the area of large phylogenetic trees. Lessons learned from the last decade include that approaches should be technology agnostic, use standard web technologies or deliver a complete solution. Independent of the technology, the major driver for science gateways are the user communities and user engagement is key for successful science gateways. The US Science Gateways Community Institute (SGCI), opened in August 2016, provides free resources, services, experts, and ideas for creating and sustaining science gateways. It offers five areas of services to the science gateway developer and user communities: the Incubator, Extended Developer Support, the Scientific Software Collaborative, Community Engagement and Exchange, and Workforce Development. The talk will give an introduction to science gateways, examples for science gateways & an overview on the services offered by the SGCI to serve user communities & developers for creating successful science gateways.

Discover UCIT Research Computing Tools and Services

 

 

 

 

UC Celebration of National GIS Day

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Please mark your calendars on November 14, 2018 as UC Libraries will join the Department of Geography & GIS, GISSA and the Geography Graduate Student Association in celebrating National GIS Day.

This year’s speaker will be Dr. Daniel Sui , Vice President for Research, University of Arkansas and former Division Director for Social and Economic Sciences (SES) at the U.S. National Science Foundation.

Agenda:

Venue – 402 Braunstein Hall

10:00 a.m. – 11:00 a.m. Open meet and greet

Venue – TUC 427

11:00 a.m. – 12:00 p.m. Lunch

12:00 p.m. – 1:00 p.m. Featured Speaker: Dr. Daniel Sui

1:00 p.m. – 2:00 p.m. Question and Answer Session

This event is free and open to all

Flyer – UC_GIS_Day

Second Mapathon to be held at UC Libraries – Nov 3rd, 2018

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missing maps banner

 

 

 

 

 

 

On Nov 3rd, The Red Cross will hold their second Missing Maps Mapathon at UC Libraries in 475 Langsam from 10 am to 2 pm.  The information collected from a Mapathon helps the Red Cross identify the best locations to bring in emergency supplies, where to house emergency operations and what local resources they can collaborate with in emergency response efforts.  In order to participate, you do not need extensive mapping experience.  The maps are creating using the Open Street Map platform and you can learn quickly by watching these training videos (1. Create an Open Street Map account, 2. Learn to map buildings).

If you are interested to participate, please register here –  https://goo.gl/forms/b2sAl9zlS4ajSklg1  and watch the training videos.  A Pizza lunch will be provided for attendees.  Please bring a drink or refillable water bottle.  This is a great and fun way to get service hours if you need them.

Please contact Amy Koshoffer – ASKDATA@UC.EDU if you have questions about the event.  More information is provided in the attached flyer.

Flyer – Missing Maps Flyer rev. 10.3.18

Jetstream Hands-on Workshop October 31st

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Indiana University’s Jeremy Fischer will present a hands-on workshop on Jetstream, a free, cloud-based, on-demand high performance computing resource.
Please join IT@UC R&D and UCL on October 31 from 9:30am to 12:30pm in Langsam Library room 475 for a free workshop on Jetstream, the National Science Foundation’s first science and engineering cloud. With a focus on ease of use and broad accessibility, Jetstream is designed for those who have not previously used high performance computing and software resources.

Jetstream Core capabilities

  • Interactive virtual machines (VMs) – both a public library of preconfigured VMs and a private library with saved, personalized versions
  • Secure data movement using Globus Transfer
  • Virtual desktops for access from a tablet or laptop over a cellular network
  • Reproducible data analysis using digital object identifiers (DOIs) stored and published via IU’s digital archive

Workshops are open to anyone who interested in learning about Jetstream resources. There are no prerequisites for attending. Please bring a lap top.   REGISTER

Flyer: jetstream_oct_31

For additional information, contact Jane Combs at combsje@uc.edu.

After the workshop head to the Catskeller for the first Data Science Social from 4-6 pm.  Food provided through the Provost funded Data & Computational Science Series.  Drinks on you!

Visiting Librarian Yanli Liu Gave Her Final Presentation

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Yanli Liu gave a presentation about data services and courses at the National Science Library, China Academy of Sciences

Yanli Liu and Amy Koshoffer co-taught a session for summer research students.

Hong Cheng, Ted Baldwin, Xuemao Wang, Yanli Liu, Leslie Schick at Yanli’s final presentation.

Yanli Liu, the visiting librarian from the National Science Library, Chinese Academy of Sciences completed her six-month period at the University of Cincinnati. Splitting time at the CEAS Library and the HSL Library, Yanli was involved in research data services, engineering librarianship, attending campus-wide workshops and webinars. On October 4th, she gave a final presentation about her two main projects: citation analysis of Mathematics and Physics researchers at UC and data management services survey and workshop.

 

Videos from Research Reproducibility workshops now available

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Many thanks to all who attended the UC Libraries and IT@UC  Research Reproducibility Workshops offered on Oct 3rd and 4th.  We are especially thankful to April Clyburne-Sherin, Director of Scientific Outreach for Code Ocean who came and shared her knowledge part of the Provost sponsored Data and Computational Science Series.  The videos from the workshop are available through the STRC youtube channel and at these links:

Oct 3rd – Video – Integrating reproducible best practices into biomedical & clinical research : https://www.youtube.com/watch?v=V_VBmFNXWg0 

Slides – http://bit.ly/2DToKHt

Oct 4th – Preparing your data and code for reproductive publication: https://youtu.be/TkQbtEYXuUA 

Slides – shorturl.at/iwDVY

Also many thanks to Jay Sinnard and Jace Cheeseman for capturing and creating the videos.  We are grateful for the talent and knowledge in the STRC!

If you want to discuss research reproducibility or other data related issues, please contact the UC Libraries Research and Data Services Team at ASKDATA@UC.EDU.  

XSEDE HPC Workshop: GPU Programming Using OpenACC

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XSEDE HPC Workshop: GPU Programming Using OpenACC

Free Registration (required)

Description:    The University of Cincinnati is pleased to be a remote site for the XSEDE HPC Workshop GPU Programming using OpenACC, taught by the Pittsburg Supercomputing Center. OpenACC is the accepted standard using compiler directives to allow quick development of GPU capable codes using standard languages and compilers. It has been used with great success to accelerate real applications within very short development periods. This workshop assumes knowledge of either C or Fortran programming.  Due to demand, this workshop is telecast to several satellite sites. Tentative Agenda

When:           November 6, 2018: 11am – 5pm

Location:    University Hall Room 454
51 Goodman Street
Cincinnati, OH 45221

Note:               You need an XSEDE account to register Create Account

Parking:          Kingsgate Garage, 151 Goodman Street

Special Instructions: Participants should bring their own laptop, lunch will be provided.

Questions?     Contact Amy Latessa latessak@uc.edu

XSEDE (eXtreme Science and Engineering Discovery Environment) is a virtual system that provides compute resources for scientists and researchers from all over the country. Its mission is to facilitate research collaboration among institutions, enhance research productivity, provide remote data transfer, and enable remote instrumentation. XSEDE is funded by National Science Foundation (NSF).  Getting Started Guide for XSEDE.

Flyer – DCS2-OpenACC Nov 6, 2018

 

Some Blowpipe Equipment : Notes from the Oesper Collections, No. 52, September/October 2018

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A portable Berzelius oil lamp for blowpipe analysis. The additional ring and alcohol lamp could be used to evaporate mineral water samples for analysis.

A portable Berzelius oil lamp for blowpipe analysis. The additional ring and alcohol lamp could be used to evaporate mineral water samples for analysis.

Issue 52 highlights items in the Oesper Collections related to the practice and teaching of blowpipe analysis.

Click here for all other issues from the Oesper Collections and to explore the Jensen-Thomas Apparatus Collection.

 

 

 

 

 

 

SAE Standards and Papers (Trial Access)

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Through November 10, UC has trial access to SAE Mobilus, a vast repository of engineering and technical content for the automotive, aerospace, and commercial vehicle industries.  The trial includes access to SAE standards and technical papers.

Standards cover these areas: Ground Vehicle Standards (J-Reports), Aerospace Standards, and Aerospace Material Specifications (AMS). Technical papers include thousands of reports on the latest advances and research in all areas of mobility engineering, including ground vehicle, aerospace, off-highway transport, and manufacturing technology.

Your feedback on the SAE Mobilus trial is important to our evaluation.  Please send comments to: Ted.Baldwin@uc.edu (Ted Baldwin, Director of the Science and Engineering Libraries).  Following the trial, we will use your feedback to determine if we pursue a campus subscription.

How UC Researchers use the Open Science Framework – Karlynn BrintzenhofeSzoc, CAHS-School of Social Work, Associate Professor

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In our third installment of the series “How UC Researchers use the Open Science Framework”, we hear from

Karlynn BrintzenhofeSzoc, CAHS-School of Social Work, Associate Professor

Karlynn Brintzenhofeszoc, CAHS-School of Social Work, Associate Professor

 

Research Project Description or statement about your research interest:

I am working with a group of trans-disciplinary researchers who focus on the current state of care for older adults with cancer.  It is well known that enrollment of older adults into cancer clinical trials is not proportional to the number of older adults who are diagnosed with and treated for cancer.  Further there is little known about how older patients who participated in clinical trials respond to treatments.  And we do not have a clear understanding of the many factors that affect their quality of life during treatment such as drug tolerance levels or best practices in coordinating their care.

Additionally, The American Society for Clinical Oncology (https://www.asco.org/) published a call to increase the recruitment of older adults into trials.  One of the main recommendations they made is that journals develop policies that would involve a better reporting system that would encourage data to be analyzed and reported by age groups on efficacy and adverse effects.  This change could improve clinical practice and likely improve the quality of life of older adults.

Our research project will take a snapshot of the literature and focus on Phase III therapeutic cancer clinical trials.  We are conducting a systematic review of the literature for the time frame of July 1 2016 to June 30 2017.  One of the data points we are gathering is inclusion and exclusion criteria which have an upper age cutoff.  Already we see in the literature that there is an inconsistency in age reporting.  Also, it is difficult to find reports where the results are stratified for older adults.  And in order to set best practices, we believe researchers need to pay more attention to older adults when reporting outcomes.

This group of researchers and clinicians are a part of the Cancer and Aging Research Group (mycarg.org) which is a national advocacy group that funds and supports research to provide better coordinated care for older adults with cancer.

Why did you chose to use the OSF to organize your research/projects?

We started off using another workflow to assign readings to reviewers and it was a disaster in record keeping.   We couldn’t figure out what articles had been assigned to reviewers, and if and when they had completed their assigned readings.

Then I discovered the Open Science Framework (through an email from the library) and switched to using the OSF.  It was very easy to transition our workflow to this system.  We could set up projects in the OSF, connect with the reviewers by inviting them to be collaborators, and share their tasks through the OSF.  We created files (or components in the OSF) for each person.  We loaded their reading assignments into the project and were able to track when they opened the files.  So we knew what was getting done and what still needed to be addressed.  It was very easy to use, especially for collaborators with virtually no training needed.  There was no angst or pain with the system.  It is also very easy to add and remove collaborators.

What about the OSF makes this tool a good choice for your project management (i.e. specific function of the OSF)?

I LOVE the notification features.  We can track that the work is being done by the reviewers assigned.  And it is easy to extract the data from a collection document in the OSF into our REDCap data management system.

Additional comment for the post that you are willing to share:

A second group of clinicians and researchers who are members of the Multinational Association of Supportive Care in Cancer (MASCC; mascc.org) are starting another project using the OSF.  A CARG clinicians, who is leading this second project that is looking at shared decision making with older adults with cancer, has also decided to use OSF for the project.

The OSF has a lot of potential.  I personally could use it more, but would want additional training to understand all the functionality of the OSF.  And I love that the platform is accessible anywhere.

Currently our project is only accessible to collaborators, but it will be easy to open components of the project if we choose or need to share some of our findings.