Archive for category Open Science..all its forms

Open Science for Identifying “Known Unknown” Chemicals http://dx.doi.org/10.1021/acs.est.7b01908

I am happy to announce the publishing of an article regarding “Open Science for Identifying “Known Unknown” Chemicals” at http://dx.doi.org/10.1021/acs.est.7b01908. I have been involved with two other articles about the identification of “Known Unknowns”.

The first one was a ChemSpider article: “”Identification of “known unknowns” utilizing accurate mass data and ChemSpider”. Journal of The American Society for Mass Spectrometry. 23: 179–185. doi:10.1007/s13361-011-0265-y.”

The second one was a recent article from the EPA: “”Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard”. Analytical and Bioanalytical Chemistry. 409: 1729–1735. doi:10.1007/s00216-016-0139-z.”

The most recent publication was a collaboration with Emma Schymanski from Eawag and it was a real pleasure to write this together. If you are interested in how Open Science can contribute to the challenges associated with the identification of known unknowns check out our latest publication!

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PRESENTATION: Building an Online Profile Using Social Networking and Amplification Tools for Scientists

This presentation was given as a 2 hour hands-on training course at the Frontier Building in the Research Triangle Park in NC funded by an Industry Award Grant from the ACS and matching financial support from the Research Triangle Institute.

Abstract “Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools such as Facebook, Twitter or other related websites. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our careers. We are already being indexed and exposed on the internet via our publications, presentations and data and new “AltMetric scores” are being assigned to scientific publications as measures of popularity and, supposedly, of impact. We now have even more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation provides an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. It will discuss the new world of AltMetrics that is in an explosive growth curve and will help you understand how to influence and leverage some of these new measures. Participating online, whether it be simply for career advancement or for wider exposure of your research, there are now a series of web applications that can provide a great opportunity to develop a scientific profile within the community.”

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Social Media Tools for Scientists and Building an Online Profile

This presentation will be given at the Janelia Farm Research Campus, a research campus of the Howard Hughes Medical Institute. The presentation abstract is below.

ABSTRACT
Despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our careers. We are already being indexed and exposed on the internet via our publications, presentations and data and new “AltMetric scores” are being assigned to scientific publications as measures of popularity and, supposedly, of impact. We now have even more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation provides an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. It will discuss the new world of AltMetrics that is in an explosive growth curve and will help you understand how to influence and leverage some of these new measures. Participating online, whether it be simply for career advancement or for wider exposure of your research, there are now a series of web applications that can provide a great opportunity to develop a scientific profile within the community.

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My NC-ACS Distinguished Speaker Award Presentation

Last night I was honored to receive an award from the North Carolina Local Section of the American Chemical Society. I had the chance to review the past 20 years of my career with the attendees. I assembled a slide deck from about ten years of slides stored on Slideshare (I am glad I have been storing them there as it’s a great online storage place!). I appreciate the recognition from the Local Division. THANKS!

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NCSU Presentation: Data integration and building a profile for yourself as an online scientist

This is a presentation I gave at North Carolina State University hosted by Denis Fourches.

Data integration and building a profile for yourself as an online scientist

Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our future careers. We are being indexed and exposed on the internet via our publications, presentations and data. We also have many more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. Many of these can ultimately contribute to the developing measures of you as a scientist as identified in the new world of alternative metrics. Participating offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.

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Give me kudos for taking responsibility for self-marketing my scientific publications and increase impact

This presentation was given at the ACS Denver meeting on March 22nd 2015 in a CINF Division symposium

Give me kudos for taking responsibility for self-marketing my scientific publications and increase impact.

Antony Williams, Will Russell, Melinda Kenneway and Louise Peck

The authoring of a scientific publication can represent the culmination of many tens if not 100s of hours of data collection and analysis. The authoring and peer-review process itself often represents a major undertaking in terms of assembling the publication and passing through review. Considering the amount of work invested in the production of a scientific article it is therefore quite surprising that authors, post-publication, invest very little effort in communicating the value and potential impact of their article to the community. Social networking has clearly demonstrated the ability to self-market and drive attention. At the same time, the increasing volume of literature (over a million new articles are published every year), requires authors to take on a more direct role in ensuring their work gets read and cited. This requirement may grow with the emergence of a range of metrics at the article level, shifting attention away from where a researcher publishes to the performance of their individual articles. Therefore, a separate platform to facilitate social networking and other discovery tools to communicate the value of published science to the community would be of value. In parallel the possibility to enhance an article by linking to additional information (presentations, videos, blog posts etc) allows for enrichment of the article post-publication, a capability not available via the publishers platform. This presentation will provide a personal overview of the experiences of using the Kudos Platform and how it ultimately benefits my ability to communicate an integrated view of my research to the community.

 

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Pacifichem: The Increasing Influence of Openness in the Domain of Chemistry (#325)

Pacifichem 2015 will see me co-hosting two sessions at the meeting. The first one is described here,The Evolving Nature of Scholarly Communication: Connecting Scholars with Each Other and with Society“, and the second one is “The Increasing Influence of Openness in the Domain of Chemistry“.

The call for abstracts is open for BOTH sessions now until April 3rd. I believe that the majority of readers of this blog almost certainly would be interested in attending these sessions and hopefully contributing to them so please submit your abstracts soon before the deadline expires!

Outline of the Session:

Chemists are being impacted by openness every day. Open Access publishing is being encouraged by various funding agencies that support our work, we are using open source code on a daily basis, whether we know it or not, and we are increasingly accessing open data via Internet searches. The proliferation of open science is providing access to an increasing number of free and re-usable data sources for chemistry. Crowdsourcing platforms allow chemists to contribute data, annotations and assertions, including chemical compounds, reaction schema, and analytical data. Collectively these data are facilitating education, enhancing discoverability and underpinning decision making in the laboratory. Through this symposium we aim to bring together participants serving up resources for the community and engage the audience in reviewing the success, opportunities and future of open science in its various forms. The future development of science will be increasingly impacted by the open contributions and innovation and chemistry in particular is one of the scientific domains presently gaining momentum

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A presentation at Research Square: The Benefits of Participation in the Social Web of Science

Yesterday I had the privilege of giving a presentation at Research Square in Durham. In terms of an audience, and an environment to present, it was certainly an ideal environment and very recipient audience….but how could it not be with their mission being to provide “research communication without roadblocks”. As the MC for the day commented about when she joined Research Square “I thought “I’d found my peeps””. So many of the conversations over lunch were about commonality of views..and it appears…our networks are so similar….yup, definitely my type of peeps. 🙂

If you don’t think you know Research Square then maybe you know some of their brands? Rubriq, Journal Guide and American Journal Experts.

The Benefits of Participation in the Social Web of Science

With the flourishing environment of platforms for sharing data, establishing an online profile and engaging in scientific discourse through alternative modes of publishing and participation, there are numerous potential benefits. However, while many scientists invest significant amounts of time in sharing their activities and opinions with friends and family the majority do not make use of the new opportunities to participate in the developing social web of science, despite the potential impact and influence on future careers. We now have many new ways to contribute to science outside of the classical publishing model. These include the ability to annotate and curate data, to “publish” in new ways on blogs and micropublishing sites, and many of these activities can be as part of a growing crowdsourcing network. Our efforts in this area are already being indexed and exposed on the internet via our publications, presentations and data and increasingly we are being quantified. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose their scientific activities online. Many of these can ultimately contribute to the developing metrics of a scientist as identified in the new world of alternative metrics. Participation offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.

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A chemistry data repository to serve them all

A presentation that I am giving around UK universities in September/October 2014

A chemistry data repository to serve them all

Over the past five years the Royal Society of Chemistry has become world renowned for its public domain compound database that integrates chemical structures with online resources and available data. ChemSpider regularly serves over 50,000 users per day who are seeking chemistry related data. In parallel we have used ChemSpider and available software services to underpin a number of grant-based projects that we have been involved with: Open PHACTS – a semantic web project integrating chemistry and biology data, PharmaSea – seeking out new natural products from the ocean and the National Chemical Database Service for the United Kingdom. We are presently developing a new architecture that will offer broader scope in terms of the types of chemistry data that can be hosted. This presentation will provide an overview of our Cheminformatics activities at RSC, the development of a new architecture for a data repository that will underpin a global chemistry network, and the challenges ahead, as well as our activities in releasing software and data to the chemistry community.

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Accessing 3D Printable Chemical Structures Online at #ACSsanfran

This presentation was given by Vincent Scalfani and covers the work we have done to provide access to 3D printable chemical structures online…

Accessing 3D Printable Chemical Structures Online

We have been exploring routes to create 3D printable chemical structure files (.WRL and .STL). These digital 3D files can be generated directly from crystallographic information files (.CIF) using a variety of software packages such as Jmol. After proper conversion to the .STL (or .WRL) file format, the chemical structures can be fabricated into tangible plastic models using 3D printers. This technique can theoretically be used for any molecular or solid structure. Researchers and educators are no longer limited to building models via traditional piecewise plastic model kits. As such, 3D printed molecular models have tremendous value for teaching and research. As the number of available 3D printable structures continues to grow, there is a need for a robust chemical database to store these files. This presentation will discuss our efforts to incorporate 3D printable chemical structures within the Royal Society of Chemistry’s online compound database.

 

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