Interested in doing reproducible research? Have you tried protocols.io?

Protocols.io is a secure platform for developing and sharing reproducible methods.

Chemistry protocols

Protocols.io is keen for researchers in chemistry and related fields in the physical sciences to use their platform to create and share their protocols. Here are a couple of examples:

https://www.protocols.io/view/spectrophotometry-method-for-the-detection-of-bioc-6wchfaw

https://www.protocols.io/view/measuring-leaf-carbon-fractions-with-the-ankom2000-yinfude.

Features of protocols.io

It is free to create an ‘Open Research’ account which allows you to publicly share unlimited protocols. Every new protocol starts out private. You can then choose to keep it private, share it with others, or make it public. Collaboration with other scientists is therefore possible.

You can use the Editor to create protocols, documents, or collections, including concurrent editing for teams.

You can use Workspaces to share files and reagent library, including secure file sharing, individual and workspace commenting features.

Using File Manager to support any file type allows archiving, auditing, exporting, including connection to DropBox, One Drive.

You can Run protocols as checklists, any changes you make are recorded in your File Manager. Experiments can be kept private or share them with others.

Individual protocols show all the steps involved, including an abstract, and you can insert images. You can link to the materials required. You can view the metadata for the protocol in various formats including DOI, PDF, HTML, external link, protocol citation, manuscript citation, and protocols are published open access as CC-BY. There is even a widget and QR code for each protocol that you can use to easily share and promote it. You are also able to view the metrics for a protocol (views, exports, steps, runs).

Authors of a protocol can copy it, if making a duplicate is useful. Authors and other users can fork protocols to receive an editable version that can be modified to their needs. Authors can also create a version of a protocol to give them an editable version and allows them to keep the protocols up to date, correct mistakes or add updates. All versions of a protocol are linked together, allowing others to see the most recent and earlier versions.

When you Publish a protocol, you will receive a DOI, which is archived with CLOCKSS to ensure long term preservation. You can link protocols to published papers.

Want to find out more?

There is much more information available on how to use protocols.io on their website. Why not create a free account and experiment?

We would be happy to set up a demo of protocols.io for you and your colleagues. To arrange this please contact the Chemistry Librarian, Clair Castle, at cmc32@cam.ac.uk.

Cambridge Data Week 2020

How are you managing the data and information generated through your research? Are we on the right track with our data practices, or do we need to see greater shifts in behaviour and research culture? 

To help you think through those questions, the Office of Scholarly Communication at Cambridge University Libraries is delighted to announce 

Cambridge Data Week, Monday 23 – Friday 27 November 2020, 

a week-long webinar series featuring topics surrounding the research data management landscape, designed for University of Cambridge researchers in all disciplines and those working in research support.  

In this series of talks, panel discussions and interactive Q&A sessions, we will explore and debate different approaches to research data management with researchers, funders, publishers and other stakeholders. Each day we will address key questions on specific topics, including:  

• innovative ways of supporting researchers with data management 
• sustainable models and levels of expectation for peer reviewers when it comes to data 
• successes and future trends in data reuse 
• the relationship between reproducibility and data management. 

All events will offer the opportunity for questions from the audience and we invite you to join discussions. 

Find full details here.  

Registration 

The events are open to all and are free of charge. They will be hosted on Zoom and require prior registration. To read full details about each session and to register, follow the links in the programme below – if you would like to submit questions in advance, you will have the opportunity at the point of registration. 

Take part in the discussions on Twitter using #CamDataWeek2020. 

Programme 

Who are the winners and losers of good data practices? 

Mandates for data sharing have been the norm for several years now but do we know what this has achieved? Data sharing and subsequent reuse has been estimated to save billions of pounds in research funding – are we getting there? Does one answer fit all – what about disciplinary differences between STEM, social sciences, arts and humanities?  

Georgie Humphreys (Wellcome Trust), Catriona MacCallum (Hindawi) and Sacha Jones (Cambridge University Libraries) tackle the tough questions.  

Monday 23 Nov 2020, 14:30-15:30 GMT 

Who is reusing data? Successes and future trends  

Reuse of data has long been argued as a central benefit of data sharing, allowing others access to a wealth of research and making research funding more efficient by removing the need to duplicate work. What do we know about the current state of play around data reuse, and what can researchers can do to increase the reuse potential of their data?   

Tiberius Ignat (Scientific Knowledge Services), Louise Corti (UK Data Archive) and Dominic Dixon (Cambridge University Libraries) lead the discussion.  

Tuesday 24 Nov 2020, 14:30-15:30 GMT 

Is data management just a footnote to reproducibility?  

Research Data Management (RDM) and reproducibility are both part of the open research ecosystem, yet the former is often viewed as another administrative burden by researchers and the latter is an important driver that has enjoyed increasing popularity since the term ‘reproducibility crisis’ was coined.  

Explore the relationship between reproducibility and RDM with Alexia Cardona (University of Cambridge), Lennart Stoy (European University Association), Florian Markowetz (University of Cambridge & UK Reproducibility Network), René Schneider (Geneva School of Business Administration) and Beatrice Gini (Cambridge University Libraries).  

Wednesday 25 Nov 2020, 14:30-15:30 GMT 

Supporting researchers on data management – do we need a fairy godmother? 

How should researchers’ data management activities and skills be supported? What are the data management responsibilities of the funder, the institution, the research group and the individual researcher?  

Tao-Tao Chang (Arts and Humanities Research Council), Marta Teperek (TU Delft Library), Al Downie (University of Cambridge) and Sacha Jones (Cambridge University Libraries) explore different implementations of support in the UK and in Europe.  

Thursday 26 Nov 2020, 14:30-15:30 GMT 

How do we peer review data? New sustainable and effective models 

The peer review process around data is still emerging, despite the increase in data sharing. What are the benefits of reviewing data to the research community, researchers and journals? What types of data are being reviewed, beyond the ‘traditional’ spreadsheets of quantitative data, and what can we learn from new models of data reviews? How can we make the work of reviewing data sustainable, and the responsibility equitably shared?   

Stephen Eglen (University of Cambridge), Kiera McNeice (Cambridge University Press), Lauren Cadwallader (PLOS) explore peer review of data from both the perspective of a publisher and that of a researcher.  

This invitation is sent on behalf of the Research Data Team at the Office of Scholarly Communication, Cambridge University Libraries. Any questions about Cambridge Data Week can be directed to info@osc.cam.ac.uk and a member of the data team will get back to you. 

How to get free (and legal) access to journal articles behind paywalls: the Open Access Button

Please have a read of this brilliant post by Lizzie Sparrow. Hopefully it can help you locate and use open access material more easily.

ChemRxiv Beta open for submissions

ChemRxiv is a free online submission, distribution, and archival service for unpublished preprints in chemistry and related areas.

ChemRxiv is now available in a fully functioning Beta version for use and feedback by researchers. Find out more from this ACS press release: https://www.acs.org/content/acs/en/pressroom/newsreleases/2017/august/chemrxiv-beta-open-for-submissions-and-powered-by-figshare.html?hootPostID=c5c5e00bed4e6b0db448b1ba9bc18551.

ChemRxiv itself can be found here.

 

Convert your files containing experimental data into an open data format

As part of the Data Champions initiative, we invite members of the Department of Chemistry to contribute to a list of instructions for converting the data you generate through experiments using techniques such as NMR spectroscopy, mass spectrometry, electron microscopy, x-ray crystallography etc. into open data formats that can be shared easily.

The aim is to save researchers time and effort in trying to find this out themselves, and to make it as easy as possible for them to share their data in an open format that is accessible to everyone.

First on our list are very brief instructions for converting NMR spectroscopy data from TopSpin to a text file in the internationally accepted open data format JCAMP-DX.

Please send your instructions to library@ch.cam.ac.uk and they will be added to the list.

Data Champions at the Department of Chemistry

Data Champions are local experts on research data management and sharing who can provide advice and training within their departments.

Your Data Champions currently are:

• Sergio Cuesta (Sergio.MartinezCuesta@cruk.cam.ac.uk, also based at the Cancer Research UK Cambridge Institute, Balasubramanian Group)
• Kent Griffith (kg376@cam.ac.uk, Grey Group)
• Quentin Peter (qaep2@cam.ac.uk, Knowles Group)

We are currently planning research data management related activities that we can carry out in the department. Please let us have your ideas! Contact one of the Data Champions or Clair Castle, Librarian at the Department of Chemistry at library@ch.cam.ac.uk.

Please visit the Chemistry Library’s Open Data website to find out more about your Data Champions, and other resources that will help chemists do open research.

Make your data and papers open via Symplectic

Open Access and Open Data are changing: Share everything via Symplectic

Demo of new system in the Pfizer Lecture Theatre for members of the Department of Chemistry on 28th February at 13:15

The current Open Access and Open Data services are being integrated with Symplectic Elements, which will bring many benefits to researchers, administrators and the Open Access and Open Data staff. The new system is live and we are asking researchers at the Department of Chemistry to start using it now. The benefits of the new system include:

• you can deposit your data and articles in one place
• you will instantly receive a placeholder DOI for data
• your outputs get into the repository quicker, which increases their visibility
• you enter the information about your publication once but it is used in many systems saving you time in the future
• better reporting capabilities for the Open Access/Data, which means more accurate reports for Departments, Faculties and Schools
• all research outputs can be uploaded to the repository via the new system

Come and see the new system being demonstrated and find out more about using it for all your research outputs. The demo will take approximately 30 minutes and there will be time for questions and answers.

Find out more here: http://osc.cam.ac.uk/open-research/symplectic-elements-deposit-pilot

We look forward to seeing you there!

Thing 19 – Text and Data Mining — 23 Research Things Cambridge

Text and data mining (TDM) is a process through which large amounts of information can be analysed electronically. This allows researchers to work through far more research content than they would ever be able to do manually. Interested and want to learn more? Well check out our brief intro video below and then get cracking […]

via Thing 19 – Text and Data Mining — 23 Research Things Cambridge

Call for Research Data Ambassadors

Do you have a passion for data? Are you a GitHub ace or an Open Data advocate? Would you like to share your expertise with others?

The Research Data Team is looking for Data Champions in departments, institutes and colleges who can advocate for managing and sharing research data in their local communities.

It is worthwhile considering participating in for anyone with a keen interest in Research Data Management (RDM) and who would like to be the local RDM expert in the department.

There is more information on the Research Data Management website: http://www.data.cam.ac.uk/datanews/call-data-champions.

American Chemical Society announces intention to establish “ChemRxiv” preprint server to promote early research sharing

What do chemists think about this? Let me know!

Electronic Collection Management

WASHINGTON, Aug. 10, 2016 — The American Chemical Society (ACS) today announced its intention to form ChemRxiv, a chemistry preprint server for the global chemistry community, proposed as a collaborative undertaking that will facilitate the open dissemination of important scientific findings. The Society is presently in the process of inviting interested stakeholders to participate in helping to shape the service ahead of its anticipated launch.

“ChemRxiv is expected to follow the established models of arXiv in physics and bioRxiv in the life sciences by enabling researchers working across diverse areas of inquiry to share early results and data with their scientist-colleagues ahead of formal peer review and publication,” says Kevin Davies, Ph.D., who, as Vice President within the ACS Publications Division, will be spearheading the effort as part of a joint undertaking with the Society’s Chemical Abstracts Service. “Preprints are fully citable and are freely accessible preliminary communications…

View original post 434 more words

Open Data at Cambridge – programme of events

The University’s Open Data team has an ever-expanding programme of events relating to all things open data in the Events section of their website at: http://www.data.cam.ac.uk/events. It’s worth bearing in mind in case you need guidance on managing and sharing your data at any point.

Useful and interesting events coming up include a data management plan clinic, open data lunchtime session, and a research data management workshop, as well as sessions on software licensing and sharing your software, copyright, and information security – all within a data sharing environment.

Guide to open science publishing by F1000Research

The recently published F1000Research Guide to Open Science Publishing gives a compact, clear and easy-to-understand basic guide on open science publishing.

It includes the chapters:

• Open access explained
• The merits of open peer review
• Understanding post-publication peer review
• What is open data?
• What is open science?
• About F1000Research

You can download, print, and share the PDF with colleagues!