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Workshops on Research Reproducibility

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Research Reproducibility Workshops

workshops facilitator April Clyburne-Sherin

workshops facilitator April Clyburne-Sherin

UC Libraries and IT@UC are pleased to offer two workshops on Research Reproducibility as part of the Data and Computational Science Series.  We are partnering with Code Ocean to offer these workshop on Oct 3rd and 4th.  The workshops facilitator is April Clyburne-Sherin from Code Ocean.  April is an epidemiologist, methodologist and expert in open science tools, methods, training and community stewardship. She holds an MS in Population Medicine (Epidemiology). Since 2014, she has focused on creating curriculum and running workshops for scientists in open and reproducible research methods and is co-author of FOSTER’s Open Science Training Handbook. She is currently the Director of Scientific Outreach for the reproducibility platform Code Ocean.  Code Ocean (https://codeocean.com/) is a cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover and run code published in academic journals and conferences.  Their mission is to make the world’s scientific code more reusable, executable and reproducible.  More information and registration for the workshops can be found at the links below.  Questions?  Email AskData@UC.Edu.  The events are free and open to all.

Workshop 1 — East Campus, Biomedical and Clinical Focus

URL – https://webapps2.uc.edu/ce/FacDev/Workshops/Details/11432

Title: Integrating reproducible best practices into biomedical and clinical research: A hands-on workshop for researchers – Data And Computational Science Series

Date: Wednesday, Oct. 3, 1 – 3pm

Location: Troup Learning Space Conf Rm-MSB G005G

Workshop 2 — West Campus, General Audience

URL – https://webapps2.uc.edu/ce/FacDev/Workshops/Details/11433

Title: Preparing your data and code for reproducible publication: A hands-on workshop for researchers – Data And Computational Science Series

Date: Thursday, Oct. 4, 10am – 12pm

Location: CEAS Library Classroom 850D Baldwin

DCS2 CodeOcean_flyerV2

 

How UC Researchers use the Open Science Framework – Emily Kean

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As the first installment of the series “How UC Researchers use the Open Science Framework”, we hear from Emily Kean, Research and Education Librarian and Liaison for Nursing who is based at the Health Sciences Library.

Research Project Description or statement about your research interest I’m incorporated on several research teams from UC Health and the College of Nursing that are conducting systematic or integrative reviews. I’m responsible for generating reproducible search strings that will eventually be published as part of the review manuscripts.

Why did you chose to use the OSF to organize your research/projects? I needed an organization tool that allowed me to track my progress over time and also share my work privately with the entire research team. I used one or two other options before settling on the Open Science Framework. OSF seems to work best for my needs. Adding collaborators is very easy and the design is so intuitive, there isn’t much of a learning curve for training new team members.

What about the OSF makes this tool a good choice for your project management (i.e. specific function of the OSF)? I love the wiki and the fact that multiple people can edit and view the same content simultaneously. Most of my process is documenting term harvesting and testing and the wiki has been the perfect way to organize my work. My research partners can see my progress in real time, and at the end, I have reproducible search strings.

Additional information about the project or using the OSF that you are willing to share: None of my projects are currently public, but one of the features of the OSF that I’m looking forward to using is sharing my sites publicly after our manuscripts are published. Typically, only one search string for a systematic review would be printed, and the OSF will allow me to share all of the progress and multiple completed strings with other interested researchers.

 

BioCyc Microbial Genomes and Metabolic Pathways Web Portal

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BioCyc Database Collection Logo

 

 

 

The BioCyc Microbial Genomes and Metabolic Pathways Web Portal is coming to the University of Cincinnati.

Beginning August 31st, researchers can access the full suite of databases in the BioCyc Database Collection. The BioCyc web portal from SRI International contains genome and metabolic-pathway information for over 10,000 microbes. BioCyc encyclopedias are unique in integrating a diverse range of data and providing a high level of curation for important microbes. BioCyc Pathway/Genome Databases (PGDB) describe the genome of an organism, as well as its biochemical pathways and (for a small fraction of organisms) its regulatory network. BioCyc bioinformatics tools combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of its extensive and complex data.

BioCyc databases integrate extensive data for each organism, and provide platforms for analysis of large-scale datasets. BioCyc enables scientists to pursue several use cases:

  • BioCyc is a massive encyclopedic reference on microbial genes, metabolites, and pathways that integrates information from many sources. Scientists consult BioCyc to save large amounts of time finding, understanding, and synthesizing material from the primary literature.
  • BioCyc is a genome informatics and comparative genomics platform.
  • BioCyc enables exploration of a vast set of biological networks.
  • BioCyc provides gene-expression, metabolomics, and multi-omics analysis tools.
  • BioCyc provides executable metabolic models for a small but growing set of organisms.

BioCyc Informatics Tools

  • Search for genomes by name, taxonomy, phenotypic properties.
  • Gene information page
    • Retrieve amino-acid sequence and nucleotide sequence of arbitrary genome region.
    • Query genes by gene name, accession number, sequence length, replicon position, protein properties (pI, MW, protein features, subcellular location, ligand), GO terms.
  • Transcription-unit information page.
  • Genome Browser depicts genomic regions at user-selected resolution with semantic zooming that reveals new features at higher resolutions. Visible features include pseudogenes, promoters, transcription-factor binding sites, repeats, terminators, nucleotide sequence. Zoom to sequence. Generate genome poster.
  • BLAST search sequence-pattern search via patmatchMap SNPs to genes and show effects on translation.

Access this URL for more information about BioCyc databases and features: https://biocyc.org/intro.shtml.

Some additional links that may be helpful:

Webinars: https://biocyc.org/webinar.shtml

Guided tour: https://biocyc.org/samples.shtml

User guide: https://biocyc.org/PToolsWebsiteHowto.shtml

Data Sheet: BioCyc data sheet

Questions?

Contact:

Tiffany J. Grant, PhD
Interim, Assistant Director for Research and Informatics
Research Informationist
Co-Leader, Research Services
Health Sciences Library
Office: (513) 558-9153
E-mail: joffritm@ucmail.uc.edu
Web: http://libraries.uc.edu/digital-scholarship/data-services.html

The Open Science Framework – a tool to help you organize and collaborate on research projects

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Welcome back to campus!  As you begin to plan out your research projects or continue on going research, you may find a need to tie down all the working parts of your projects.  One tool that can help you is the Open Science Framework.  This tool developed by the Center for Open Science is a easy to use platform that allows you to create a structure to organize projects, invite collaborators, share within your research group and with the research community at large.  The mission of the COS is to promote transparency and reproducibility in research through practice and resource development.  Though the words open and science appear in the name, the projects you manage within the OSF are private from the start and made only public if you choose to share.  And you can share a part or all of the project as you wish.  And it is not just a STEM platform.  Any group needing to organize a project can use the OSF.  UC has a dedicated portal to the OSF at https://osf.uc.edu .

Over the next few weeks, stop back to Liblog to learn more about how UC researchers are using the OSF to facilitate their research projects.

Dean’s Corner: Welcome Back UC!

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I am currently visiting Kuala Lumpur, Malaysia for the International Federation of Library Associations and Institutions (IFLA) World Library and Information Congress along with some of my colleagues from UC Libraries, but I’m excited to return to UC and greet our new and returning students and faculty.

At IFLA’s World Conference with Library Chief Technology Officer May Chang and Global Services Librarian Hong Cheng. Behind us is Kuala Lumpur’s famous Petronas Towers.

Before we dive into the fall semester, here’s a brief overview of the last few months at UC Libraries.

Several key library positions were filled over the summer, including: associate director of business affairs Jeremy Berberich; business and data analytics librarian Maggie Patel; associate dean of library services Brad Warren; and content analyst Dorcas Washington. The Digital Scholarship Center also continued to grow, welcoming digital scholarship library fellow Erin McCabe and data visualization developer Ezra Edgerton. They joined software developer Zhaowei Ren, with the support of a grant from the Andrew W. Mellon Foundation.

UC Libraries joined HathiTrust, a national and international partnership of research institutions and libraries.

The Winkler Center Advisory Board hosted the annual Cecil Striker Society Lecture, “Cincinnati Children’s Hospital Impacting the Health of Children in Our Community and the World: The Past, Present and Future,” with co-lecturers Michael K. Farrell, MD and Bea Katz, PhD.

Continue reading →

XSEDE HPC Workshop: BIG DATA – Data & Computational Science Series

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As part of the Data and Computational Science Series funded by the Provost Office, IT@UC and UC Libraries will host the XSEDE HPC Workshop: BIG DATA workshop.  

The University of Cincinnati is pleased to be a remote site for the XSEDE HPC Workshop on Big Data. This 2-day workshop will focus on topics including Hadoop and SPARK. Please bring a lap top, lunch will be provided both days.

When: Wednesday and Thursday September 5-6, 2018; 11am – 5pm

Location: University Hall 4th floor suite, Room 420B

Free Registration (required) Click Here!

Note: You need an XSEDE account to register: Create Account

Tentative Schedule (Eastern Standard Time)

Special Instructions: Participants should bring their own laptop, no previous HPC experience needed, lunch will be provided.

Parking: Kingsgate/University Hall Parking Garage or UC North Shuttle

DCS2 XSEDE BIG DATA flyer1

Questions? Contact Jane Combs at combsje@ucmail.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.

Native Voices: Keynote Presentation and Exhibit Opening

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Suzanne Singer gives the keynote address to kick off the Native Voices exhibit.

On Thursday, July 26, Dr. Suzanne Singer launched the Native Voices exhibit opening giving her keynote presentation after introductions by Xuemao Wang, Dean, University of Cincinnati Libraries; Philip Diller, MD/PhD, Chair and Fred Lazarus Jr Endowed Professor of Family and Community Medicine; and Bleuzette Marshall, PhD, Vice President for Equity and Inclusion at UC. Dr. Singer is an Energy Systems and Thermal Analyst in the Computational Engineering Division at the Lawrence Livermore National Laboratory in Livermore, CA.  Her talk focused on the intersections between land, energy, and health in the Navajo community.

After the presentation attendees were encouraged to visit the exhibit and enjoy some of the catered hors d’oeuvres. In addition to the Native Voices exhibit, which is made up primarily of oral histories, a supplementary poster presentation also will run concurrently with the exhibit and be on display alongside the Native Voices listening stations. The posters are a capstone project from a UC Medical Botany class taught by Theresa M. Culley, Ph.D. and Eric Tepe, Ph.D during spring semester, 2018. The posters examine how Native Americans used indigenous plants to maintain health and hygiene.

Panels in the Native Voices: Native Peoples’ Concepts of Health and Illness exhibit.

Do try to attend one of the Native Voices lectures over the next several weeks. On Wednesday, August 8th, Madeleine Fix will present “Cincinnati’s Public Landing, the Measles, and Wyandot Removal.”  If you are unable to attend, stay turned for more recaps.

A schedule of the remaining lectures is available online. And thank you so much for your continued support of this exhibit and its additional programming.

In the carousel below, please enjoy some of the images taken at the keynote and exhibit opening.

Native Voices Children’s Programming Event a Success

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Last week several UC Libraries (HSL, CECH, Langsam) collaborated to produce the first installment in our Native Voices: Native Peoples’ Concepts of Health and Illness public programming. This inaugural event focused specifically on children as Langsam Library received a visit from twenty-four students of the Arlitt Child & Family Research & Education Center. Cheryl Ghosh, Senior Librarian at UC’s CECH Library put together an amazing program of dramatic skits, activity stations, and multi-media fun.

First, the 3 to 5-year-olds were treated to an introduction and brief play about the Iroquois legend of the Three Sisters and its corresponding gardening tradition. This tradition of planting corn, beans and squash (the sisters) in close proximity is widespread among Native American farming. At the same time the story functions as a metaphor for supporting and helping one another.

After the skit, the children were divided into groups and each group moved on to an activity station. One group and its chaperones built a teepee. The other, shucked corn and picked beans from bean plants. After ten minutes the groups switched and tried the other activity.

After fifteen minutes of activities, the students had a brief snack then proceeded to the Student Technology Resource Center (STAC) where video was taken of them in front of a green screen. At that point the video was superimposed onto an image of the Great Plains and an American Indian village complete with moving buffalo.

Finally, as a parting gift, each child received the book D is for Drum: A Native American Alphabet by Debbie and Michael Shoulders and Irving Toddy. The event lasted approximately an hour and at no time did our worries of waning attention spans among the children materialize. They never once lost interest. A success, if we  do say so!  And a huge thanks to all who assisted.

Please plan to attend the Native Voices: Native American Concepts of Health and Illness opening event on Thursday, July 26th in the CARE/Crawley Atrium of the UC  Medical Sciences Building.  And stay tuned for the six weeks of supplementary programming the HSL has planned.

Please see the gallery below for more images of the event.

 

Visit the Exhibit “Native Voices: Native People’s Concepts of Health and Illness” on Display Now in the Donald C. Harrison Health Sciences Library

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Native Voices ExhibitNative Voices: Native Peoples’ Concepts of Health and Illness, a traveling exhibition to U.S. libraries, is on display now through August 30 on the main level of the Donald C. Harrison Health Sciences Library.

Native Voices explores the interconnectedness of wellness, illness and cultural life for Native Americans, Alaska Natives and Native Hawaiians. Stories drawn from both the past and present examine how health for Native People is tied to community, the land and spirit.

Through interviews that can be listened to via iPads located throughout the display, Native People describe the impact of epidemics, federal legislation, the loss of land and the inhibition of culture on the health of Native individuals and communities today.

 

Related Events

suzanne singerIn association with the Native Voices exhibit, related events have been scheduled to explore the topic of Native Peoples’ Concepts of Health and Illness.

The first scheduled event is keynote speaker Suzanne L. Singer who will speak on Intersections of Energy and Wellness from 5-7:30 p.m., Thursday, July 26, in the CARE/Crawley Atrium (Medical Sciences Building, 231 Albert Sabin Way).

Throughout August, lectures that cover such topics as “The Contribution of Native Voices to Medicine through Botany,” “Breaking Bread: A Perspective of Fry Bread and Native Health” and “Preventing Tuberculosis while Regulating Indigenous Bodies” have been scheduled in the Stanley J. Lucas, MD, Board Room, E level of the Medical Sciences Building near the Kresge Circle.

A full schedule of events is listed online.

 

The U.S. National Library of Medicine (NLM) developed and produced Native Voices: Native Peoples’ Concepts of Health and Illness. The American Library Association (ALA) Public Programs Office, in partnership with NLM, tours the exhibition to America’s libraries. Native Voices: Native Peoples’ Concepts of Health and Illness was displayed at the NLM in Bethesda, Maryland, from 2011 to 2015. To learn more and view content from the exhibition, visit http://www.nlm.nih.gov/nativevoices.

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And don’t miss the exhibit “The Kretschmer Collection of Native American Children’s Literature donated by Drs. Richard and Laura Kretschmer” on display on the 4th floor lobby of the Walter C. Langsam Library. The exhibit features children’s books with Native American themes, written and illustrated by Native Americans and donated by Drs. Richard and Laura Kretschmer and housed in the College of Education, Criminal Justice and Human Services Library.

Health Sciences Library Positions Available – Please Apply

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The Health Science Library is currently accepting applications for student assistants.

Positions are now open in the following Departments

  1. Circulation
  2. Winkler Center

Positions require a commitment of at least 6 – 15 hours per week.  Some positions require a Federal Work Study Grant.

The library is located, near the main elevator banks, on the E level of the Medical Science Building, on the Medical campus.

Please fill out the Library specific application.  Be sure to mark HSL as a preferred job site.

 

For questions concerning the Circulation Department,

Email: bacheldn@ucmail.uc.edu

 

For questions concerning the Winkler Center,

Email: pasigo@ucmail.uc.edu