Category Archives: HSL News

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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.

 

Bernstein, Shakespeare, Preservation Photographs and Dedicated Staff are All Featured in the Latest Issue of Source

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source headerRead Source, the online newsletter, to learn more about the news, events, people and happenings in UC Libraries.

In this edition of Source we celebrate Leonard Bernstein at 100 with news of an exhibit on display in the Walter C. Langsam Library. Dean Xuemao Wang writes about how the occasion of the university’s upcoming Bicentennial has led him to reflect on the contributions of four staff members retiring this fall. We announce two grants received by the National Network of Libraries of Medicine that will promote good data and good health.

University archivist and head of the Archives and Rare Books Library Kevin Grace teaches readers and students in his honors class about Extra-Illustrated Editions. Jessica Ebert, lead photographic technician in the Preservation Lab writes about her work creating visual representations of the conservation treatments performed, and housing created, in the Lab. Mike Braunlin of the John Miller Burnam Classics Library offers his experience and insights gained working in the library for 42 years. The UC Foundation writes about a unique collection gifted to the Libraries from two former professors. Lastly, the annual Books by the Banks: Cincinnati USA Books Festival, of which UC Libraries is an organizing partner, is announced in this issue.

Read these articles, as well as past issues, on the web at http://libapps.libraries.uc.edu/source/ and via e-mail. To receive Source via e-mail, contact melissa.norris@uc.edu to be added to the mailing list.

UCSC Genome Browser Training

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UC Logo

The University of Cincinnati Libraries Research and Data Services Group is sponsoring
University of California Santa Cruz Genome Browser Training

UCSC Genome Browser Website: https://genome.ucsc.edu/

UCSC Genome Browser Logo

Morning Sessions (October 30th and 31st 9am – Noon) 

Locations:

October 30th MSB 5051 9am-noon and October 31st MSB 7051 9am-noon

Afternoon Sessions

1-4pm October 30th and 31st HSL Troup Learning Center

Image of Robert Kuhn, Genome Browser Trainer

Robert Kuhn, Your Trainer

Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he  studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz.  He joined the UCSC Genome Browser project in 2003, where he is now Associate Director, with a particular interest in clinical  genetics.  The Genome Browser is a widely used genomics tool giving access to the genomes of human and more than one hundred  other animals.  Dr. Kuhn’s responsibilities include identifying important datasets for inclusion into the Browser, enabling  researchers through teaching the Genome Browser in workshops and seminars and learning from them how to improve the Browser.

Registration

Registration for the training is via WebEx, but you can attend the morning sessions in person or virtually. 

*Afternoon attendance is limited to in person only* 

Day1 Registration: https://bit.ly/2x7WVVk

Day 2 Registration: https://bit.ly/2OdEBS1

Afternoon Session Registration: https://webapps2.uc.edu/ce/HSL/Workshops

Please be sure to bring your own device.

UCSC Genome Browser Training Schedule

Genome Browser Training

Questions?  Please contact Tiffany J. Grant, PhD

joffritm@ucmail.uc.edu

(513) 558-9153

How UC Researchers use the Open Science Framework – UC Center for Police Research and Policy

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In our second installment of the series “How UC Researchers use the Open Science Framework”, we hear from Hannah McManus, Gabrielle Isaza, and Clair Green-Schwartz, Research Associates with the IACP / UC Center for Police Research and Policy 

Hannah McManus, Gabrielle Isaza, and Clair Green-Schwartz, Research Associates with the IACP / UC Center for Police Research and Policy

Research Project Description or statement about your research interest

The International Association of Chiefs of Police (IACP)/University of Cincinnati (UC) Center for Police Research and Policy engages in rigorous research that has practical implications for the field and is intended to serve as a national model for the way law enforcement agencies and researchers work together to help protect communities, safeguard citizens’ rights, and ensure the fair treatment of all individuals.

There is currently a gap between research and practice, and the IACP/UC Center for Police Research and Policy seeks to play an important role in closing that gap. Often times existing research does not provide actionable recommendations that can be easily translated into specific, practical policies and practices that could enhance policing. Moreover, academic researchers often do not have access to all the data that police departments have that is necessary to conduct rigorous and meaningful research on police practices. The goal of the IACP/UC Center for Police Research and Policy is to provide a path for law enforcement and researchers to work together on studies that can drive future practices and policies.

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

The IACP/UC Center for Police Research and Policy is funded by the Laura and John Arnold Foundation (LJAF). The LJAF is committed to funding research that meets the most rigorous standards of quality and transparency. As such, we make public our preregistration document for each project, which involves describing the research design in detail before the statistical analyses are performed. Further, we update the Center’s OSF profile as we gather more information on individual projects, and submit all applicable research materials onto the OSF for public viewing. At the end of our research projects, we include the findings either in the form of a written report or a link to a publication or preprint elsewhere. These findings must be freely available in some form, which removes the financial barriers that some may face when trying to access research. The Center’s OSF webpage thus provides a comprehensive overview of an entire research project from start to finish. And further, in the event that a research project does not lead to a peer-reviewed publication, posting the results at OSF serves a valuable informative purpose.

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

The OSF is a useful web platform to centralize all parts of the project from initial idea to final results. It keeps a useful history of documents for us to track changes and progress over time. Ultimately, this tool is most useful in its ability to serve as a platform for transparency in research.

Please use this link for further detail about the Center for Police Research and Policy’s research projects:

https://osf.io/f2drv/

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.