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Mozilla Science Lab Promotes Data Reproduction Through Open Access: Report from 9/10/2015 Online Meeting

Posted in Academic Publishing, Curation, Experimental validation, Methods, Open Access Journals, REAL TIME Conference Coverage Twitter's Hashtags and Handles per Presentation/session, Scientific & Biotech Conferences: Press Coverage, tagged , , , , , , , , , , , , , , , , on September 10, 2015| Leave a Comment »

Mozilla Science Lab Promotes Data Reproduction Through Open Access: Report from 9/10/2015 Online Meeting

Reporter: Stephen J. Williams, Ph.D.

Mozilla Inc. is developing a platform for scientists to discuss the issues related to developing a framework to share scientific data as well as tackle the problems of scientific reproducibility in an Open Access manner. According to their blog

https://blog.mozilla.org/blog/2013/06/14/5992/

We’re excited to announce the launch of the Mozilla Science Lab, a new initiative that will help researchers around the world use the open web to shape science’s future.

Scientists created the web — but the open web still hasn’t transformed scientific practice to the same extent we’ve seen in other areas like media, education and business. For all of the incredible discoveries of the last century, science is still largely rooted in the “analog” age. Credit systems in science are still largely based around “papers,” for example, and as a result researchers are often discouraged from sharing, learning, reusing, and adopting the type of open and collaborative learning that the web makes possible.

The Science Lab will foster dialog between the open web community and researchers to tackle this challenge. Together they’ll share ideas, tools, and best practices for using next-generation web solutions to solve real problems in science, and explore ways to make research more agile and collaborative.

On their blog they highlight various projects related to promoting Open Access for scientific data

On September 10, 2015 Mozilla Science Lab had their scheduled meeting on scientific data reproduce ability.  The meeting was free and covered by ethernet and on social media. The Twitter hashtag for updates and meeting discussion is #mozscience (https://twitter.com/search?q=%23mozscience )

Open Access Meeting Announcement on Twitter

https://twitter.com/MozillaScience/status/641642491532283904

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mozilla science lab

Mozilla Science Lab @MozillaScience

Join @khinsen @abbycabs + @EvoMRI tmrw (11AM ET) to hear about replication, publishing + #openscience. Details: https://etherpad.mozilla.org/sciencelab-calls-sep10-2015 …

AGENDA:

  • Mozilla Science Lab Updates
  • Staff welcomes and thank yous:
  • Welcoming Zannah Marsh, our first Instructional Designer
  • Workshopping the “Working Open” guide:
    • Discussion of Future foundation and GitHub projects
    • Discussion of submission for open science project funding
  • Contributorship Badges Pilot – an update! – Abby Cabunoc Mayes – @abbycabs
  • Will be live on GigaScience September 17th!
  • Where you can jump in: https://github.com/mozillascience/paperbadger/issues/17
  • Questions regarding coding projects – Abby will coordinate efforts on coding into their codebase
  • The journal will publish and authors and reviewers get a badge and their efforts and comments will appear on GigaScience: Giga Science will give credit for your reviews – supports an Open Science Discussion

Roadmap for

  • Fellows review is in full swing!
  • MozFest update:
  • Miss the submission deadline? You can still apply to join our Open Research Accelerator and join us for the event (PLUS get a DOI for your submission and 1:1 help)

A discussion by Konrad Hinsen (@khinsen) on ReScience, a journal focused on scientific replication will be presented:

  • ReScience – a new journal for replications – Konrad Hinsen @khinsen
  • ReScience is dedicated to publishing replications of previously published computational studies, along with all the code required to replicate the results.
  • ReScience lives entirely on GitHub. Submissions take the form of a Git repository, and review takes place in the open through GitHub issues. This also means that ReScience is free for everyone (authors, readers, reviewers, editors… well, I said everyone, right?), as long as GitHub is willing to host it.
  • ReScience was launched just a few days ago and is evolving quickly. To stay up to date, follow @ReScienceEds on Twitter. If you want to volunteer as a reviewer, please contact the editorial board.

The ReScience Journal Reproducible Science is Good. Replicated Science is better.

ReScience is a peer-reviewed journal that targets computational research and encourages the explicit reproduction of already published research promoting new and open-source implementations in order to ensure the original research is reproducible. To achieve such a goal, the whole editing chain is radically different from any other traditional scientific journal. ReScience lives on github where each new implementation is made available together with the comments, explanations and tests. Each submission takes the form of a pull request that is publicly reviewed and tested in order to guarantee any researcher can re-use it. If you ever reproduced computational result from the literature, ReScience is the perfect place to publish this new implementation. The Editorial Board

Notes from his talk:

– must be able to replicate paper’s results as written according to experimental methods

– All authors on ReScience need to be on GitHub

– not accepting MatLab replication; replication can involve computational replication;

  • Research Ideas and Outcomes Journal – Daniel Mietchen @EvoMRI
    • Postdoc at Natural Museum of London doing data mining; huge waste that 90% research proposals don’t get used so this journal allows for publishing proposals
    • Learned how to write proposals by finding a proposal online open access
    • Reviewing system based on online reviews like GoogleDocs where people view, comment
    • Growing editorial and advisory board; venturing into new subject areas like humanities, economics, biological research so they are trying to link diverse areas under SOCIAL IMPACT labeling
    • BIG question how to get scientists to publish their proposals especially to improve efficiency of collaboration and reduce too many duplicated efforts as well as reagent sharing
    • Crowdfunding platform used as post publication funding mechanism; still in works
    • They need a lot of help on the editorial board so if have a PhD PLEASE JOIN
  • Website:
  • Background:
  • Science article:
  • Some key features:
  • for publishing all steps of the research cycle, from proposals (funded and not yet funded) onwards
  • maps submissions to societal challenges
  • focus on post-publication peer review; pre-submission endorsement; all reviews public
  • lets authors choose which publishing services they want, e.g. whether they’d like journal-mediated peer review
  • collaborative WYSIWYG authoring and publishing platform based on JATS XML

A brief discussion of upcoming events on @MozillaScience

Meetings are held 2nd Thursdays of each month

Additional plugins, coding, and new publishing formats are available at https://www.mozillascience.org/

Other related articles on OPEN ACCESS Publishing were published in this Open Access Online Scientific Journal, include the following:

Archives of Medicine (AOM) to Publish from “Leaders in Pharmaceutical Business Intelligence (LPBI)” Open Access On-Line Scientific Journal http://pharmaceuticalintelligence.com

Annual Growth in NIH Clicks: 32% Open Access Online Scientific Journal http://pharmaceuticalintelligence.com

Collaborations and Open Access Innovations – CHI, BioIT World, 4/29 – 5/1/2014, Seaport World Trade Center, Boston

Elsevier’s Mendeley and Academia.edu – How We Distribute Scientific Research: A Case in Advocacy for Open Access Journals

Reconstructed Science Communication for Open Access Online Scientific Curation

The Fatal Self Distraction of the Academic Publishing Industry: The Solution of the Open Access Online Scientific Journals

 

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Cannabis –Marijuana-Controversy

Posted in Cell Biology, Signaling & Cell Circuits, Cerebrovascular and Neurodegenerative Diseases, tagged , , , , , , on January 4, 2013| 1 Comment »

Author: Dr Anayo Unachukwu, MBBS, LLM

Man is a net product of biology and society. His biology is pretty primordial and sluggish to changes hence he struggles with optimal adaptation to his dynamic environment. It is unsurprising that he is constantly behind the curve, given the epochal changes that are attendant to post modernism. Post modernism has largely informed a parallel discourse to that which exists within public and private institutions and bodies. This discourse has gained increased traction in the 20th and 21st century, given the haemorrhage of trust from professional relationships. As O’ Neil aptly puts it, ‘loss of trust’ is in short, a cliché of our times.[1]  The public outcry that attended this breach of trust has led to several layers of professional regulations, inspections of private and public institutions; and latterly the low level of tolerance of risk in more affluent societies. However Maynard opines that the attraction of trust as the determinant of human exchange is that it is potentially more cost-effective than the alternative.[2]

With the advent of information age, the already fragile relationship between the public on one hand and professional bodies and institutions on the other has seen further entropy and perturbation. This level of instability in the relationship was largely informed by marked reduction in information asymmetry that hitherto existed in professional relationships. The nature of these relationships is now undermined by concerns about their efficiency and the consequent need for external performance management.[3] Doctor/patient relationship is unique because of the element of information asymmetry.[4] Not anymore, the public believes that, given the reduced information asymmetry, doctors no longer know the best.  The net effect is a further distrust and uncertainty about the intentions of public and private bodies on matters affecting the greater good of the society.

It is within this backdrop that most scientific debates are conducted in the media. The sceptre of scepticism is brought to the fore by the public in navigating very complex debate. This is unsurprising, given that prehistoric man has always been adept in heuristic pursuits as rough and ready guides in making sense of it all when challenged with novel situation.

The debate on Cannabis (Marijuana)-is controversial, but unsurprising, given the heat rather than light it generates-has remained greatly polarising. Like wars, the first casualty is truth. Given Cannabis chequered history, an honest scientific discourse would hardly make the rounds due to the frontloaded emotions integral to the debate. Man being a product of sluggish biology and environment will recourse to heuristic generalisations where nuanced debate is called for.

Most clinicians in mental health-who have seen lives blighted by early childhood exposure to cannabis-are most appalled, given the way the debate on Cannabis is conducted.

Cannabis has over 70 different cannabinoid chemicals[5]. The most active being Δ 9-Tetrahydrocannabinol.This very particular chemical is largely responsible for most of the cognitive[6], emotional and psychomotor impairments associated with the use of the drug.

To further compound the discourse on Cannabis, is the difficulty in predicting with any reasonable degree of accuracy as regards to who will develop mental illness with early exposure to Cannabis in childhood. Given the paucity of scientific knowledge on this, scientific community could only resort to heuristic speculation based on epidemiological data-demographics. However, this issue is more complex, given that genetics and heredity are not in the habit of playing according to linear rules.

It is pertinent to note that a counterpoint to Δ 9-Tetrahydrocannabinol is another active chemical Cannabidiol (CBD) has anxiolytic[7] and possibly antipsychotic[8] properties. However, it is difficult to know the precise ratio of these two active ingredients in Cannabis couriered and consumed on the street.

I am not for a moment advocating that the drug war as we know it-started by Richard Nixon-is the way forward. There should be an honest debate across both opposing aisles on a practical and pragmatic solution to protect the vulnerable in our society. Was it not Ghandhi that said that you can’t shake hands with clenched fists?

[1] O’ Neil O. A question of Trust BBC Reith Lectures 2002. Cambridge: CambridgeUniversity Press, 2002.

[2] Maynard A., Bloor K. Trust and performance management in the medical marketplace; Journal of The Royal Society of Medicine vol. 96 November 2003.

[3]  Ibid.

[4] Not anymore, cf Scitovsky T. The benefits of asymmetry markets. J Econ Perspect 1990; 4 135-48. He notes that this is beneficial and it is a by-product of specialisation.

[5] Celia JA Morgan et al (2010). Cannabidiol Attenuates the Appetitive Effects of Δ 9-Tetrahydrocannabinol in Human Smoking Their Chosen Cannabis, Neuropsychopharmacology, 1879-1885.

[6] D’ Souza et al (2004). The psychomimetic effects of intravenous Δ 9-Tetrahydrocannabinol in healthy individuals: implication for psychosis. Neuropsychopharmacology 29: 1558-1572.

[7] Crippa JA et al (2004). Effects of cannabidiol (CBD) on regional cerebral blood flow, Neuropsychopharmacology 29: 417-429.

[8] Zaurdi AW et al (2006). Cannabidiol monotherapy for treatment-resistant schizophrenia. J Psychopharmacol 20: 683-686.

 

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