Category Archives: HSL News

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How UC Researchers use the Open Science Framework – Theresa Culley, Head of Biological Sciences and Professor of Biology, Editor-in-Chief Applications in Plant Sciences

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Researcher Name: Theresa Culley, Head of Biological Sciences and Professor of Biology, Editor-in-Chief Applications in Plant Sciences

In our fourth installment of the series “How UC Researchers use the Open Science Framework”, we hear from  Theresa Culley, Head of Biological Sciences and Professor of Biology, Editor-in-Chief Applications in Plant Sciences

 

Theresa Culley - 2018 Head of Biological Sciences

 

 

 

 

 

 

 

Research Project Description or statement about your research interest:

My research area in Botany focuses on plant population biology and genetics and I have a deep interest in the evolution of invasive species.  I am also very interested in publication patterns regarding research involving hotspot areas of biodiversity.  My lab has been considering the question of whether researchers from developing countries, which have the most biodiversity hotspots, receive adequate credit for their work.  We are currently working on a project examining publishing bias in the scientific literature about plant conservation genetics.  This collaboration is in partnership with UC Libraries’ Digital Scholarship Center and is one of several collaborations funded by a $900,000 Andrew W. Mellon Foundation awarded to the Center.  I am also interested in this topics in my role as Editor-in-Chief for Applications in Plant Sciences.

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

I am an advocate for data sharing and reproducible research.  In an editorial I wrote for Applications in Plant Sciences, I highlighted the many reasons to ensure access to data and major considerations behind why researchers may not want to share data.  A resource like the open science framework is an excellent tool for promoting transparency and reproducibility and advancing the field at an accelerated pace.  The OSF helps to manage the entire project and especially makes it easy to share data within our research group and with collaborators.  This is a great place to manage the active parts of a project, and link all the different tools that members of a research group use .  We also have the ability to archive data and content here and look forward to a possible integration into our Institutional Repository in the future.

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

Some of my team members prefer to use Dropbox and some are using Box.  Using the OSF makes it possible to bring all the different tools we are using under one project umbrella.  And it helps us to track activity on the project.

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

Currently our project is not public, but we hope to share components in the future.

The Center for Open Science has been a great resource for our lab and the journal Applications in Plant Sciences.  In August 2016, the journal adopted the TOP guidelines, along with its sister journal, American Journal of Botany.

Lexicomp Online & Lexicomp App Access

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Lexicomp Online

Lexicomp Online is a collection of clinical databases and clinical decision support tools that provides users with an extensive medical library.  It provides clear, concise, point-of-care adult and pediatric drug information as well as in-depth information on interactions, toxicology, and more.  Lexicomp also includes support tools like drug ID, calculators, and patient education.

Unlimited Lexicomp Online access is available in a responsive design that will resize to your device.

Lexicomp App Access

50 access codes are also available with this institutional subscription.

  • Lexicomp app registration is first come, first serve
  • This year only, app accounts expire during December of 2018

Watch for a blog post in December 2018 or January 2019 with a link to a new set of 50 access codes.

  • App registration will again be first come, first serve
  • After which app accounts will expire annually

Lexicomp Academic Discount Program

Data Science Social – Wednesday OCTOBER 31 4-6 pm

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Please Join Us Wednesday OCTOBER 31 from 4-6 pm at the UC Catskeller

Bring your Scariest Data Dilemma & Swap Spooky Science Stories with colleagues!

Sign up for a 3-minute Flash Talk here: https://goo.gl/forms/5VFzvFoUGbg1DiHq2.
RSVP and Questions: ucitresearch@ucmail.uc.edu

Food will be provided

Flyer: DCSS social flyer_20181031

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