#authorea

[ushf]

docker for ipython/jupyter

A handy way to run ipython locally. Note the re-naming of ipython to jupyter. Also note the potential handy integration with authorea<./p>

[rescomunimelb]

ResBaz Key-Stories!

At a typical academic conference keynote presenters will talk about their research. While that's all well and good, what you don't get to hear so much about is their story. How did they get to where they are today? Why are they so passionate about what they do? We've picked three of the most interesting people we know in academia and have asked them to present a "keystory" instead. Here's a little about each of them:

Monday 

Dr Jee Hyun Kim @About_Memory

Head, Developmental Psychobiology, The Florey, The University of Melbourne “Thriving under pressure: Harvest diversity"

Jee is a self-proclaimed queen of nerds whose PhD completion in Psychology at the University of New South Wales was slowed down by her dedication to saving Azeroth 2005-2008. Following a postdoctoral training at Michigan University, she moved to Melbourne to become the youngest laboratory head at the Florey Institute of Neuroscience and Mental Health. Her work focuses on the neuroscience of good and bad memories underlying anxiety and addiction in childhood and adolescence using rodent models.

She has received various awards and major grants including the University Medal in Psychology and the Australian Psychological Society early career research award. Since returning to Australia in 2011, she has won grants totalling 3 million dollars as the Chief Investigator A including Australian Research Council (ARC) Discovery Early Career Researcher Award, ARC Discovery Project Grant, National Health and Medical Research Council (NHMRC) Project Grants, and NHMRC Career Development Fellowship. In 2014 she received the Victorian Young Tall Poppy Science Award.

She strongly believes in the importance of treating mental disorders early in life, a topic she shared at TEDxMelbourne. She features regularly on radio and television to discuss memory and forgetting, and lists Beyonce, Kerrigan, and Ronda Rousey as her inspirations. She believes recruiting a diverse group of people in her laboratory as key in her success in the most difficult period of transitioning from early to mid-career scientist.

Tuesday

Angus Hervey @angushervey 

Co-Founder of Future Crunch, Manager of Random Hacks of Kindness

"What happens when you finish your PhD? Lessons from the frontline (from someone that almost didn't make it)"

Angus is a science communicator, with a background in environmental economics and international political economy. Using a combination of evolutionary psychology, history and political economy and he analyses science and technology trends and what they mean for business and society.

After an early career in Cape Town as a successful entrepreneur and lecturer, he moved to London where he managed Global Policy, a leading international publication whose advisory board included Nobel Prize winners such as Joseph Stiglitz and Amartya Sen and legendary innovators such as Muhammad Yunus and George Soros. This was an introduction to politics and economics at the highest level, and gave him an insider’s view on issues such as financial regulation, environmental management and international development.

In 2012, following the completion of his PhD as the Ralph Miliband Scholar at the London School of Economics, he moved to Melbourne. Frustrated by the lack of intelligent discussion around future trends in Australia, he co-founded Future Crunch, a forum for critical debate on the transition from the industrial to the digital era. He is also the Australian manager of Random Hacks of Kindness, a global initiative started in 2009 by Google, IBM, Microsoft, NASA and Yahoo which connects technologists with social changemakers.

Today more than ever, he combines a global perspective with the belief that change comes from small groups of people motivated by fairness, optimism and a belief in the transformative power of science and technology.

Wednesday

Alberto Pepe  @AlbertoPepe 

Co-founder of Authorea, data consultant, Research Associate at Harvard University. "On leaving academia, without ever saying goodbye" Loosely based on, https://www.authorea.com/users/3/articles/5287/_show_article

Alberto Pepe is the co-founder of Authorea, an online place to write research together. He is a "recovering academic" with previous Ph.D. and Postdoc work in Astrophysics and Information Science. He holds degrees and fellowships from Harvard, UCLA, CERN, and University College London. He was born and raised in the wine-making town of Manduria, in Puglia, Southern Italy.

[fasforward]

Copia, incolla, aggiorna: una piattaforma per cambiare il mondo della ricerca

Authorea è una piattaforma di collaborazione dedicata alla ricerca, la prima startup creata da un italiano che è riuscita a raccogliere fondi tra gli investitori di New York

[rescomunimelb]

Authorea: a review

By Damien Irving.

This post originally appeared here on my blog. We're so impressed with Authorea that we're in the process of negotiating an institutional license... we'll keep you posted!

It’s fair to say that LaTeX has gained widespread acceptance as the tool of choice for writing scientific scholarly articles (if you need convincing, see here, here and here). In comparison to a typical “what you see is what you get” (WYSIWYG) editor like Microsoft Word or Apache OpenOffice, the most radical aspect of LaTeX is that you don’t immediately see how your document will be typeset. Documents are instead prepared by writing a plain text input file that includes markup commands to specify the formatting, before invoking the LaTeX program to (typically) generate a final PDF document.

Since the LaTeX software and associated text editors like Texmaker are free to download, most scientists do all their document preparation on their own computer. While this is a perfectly valid workflow, it fails to take advantage of the fact that we now live in a web-enabled and highly interconnected world. As Alberto Pepe noted in his presentation at the I Annotate 2013 conference in San Fransisco (see below), today’s scientists are doing 21st century science, writing up using 20th century writing tools (e.g. Microsoft Word, LaTeX), then locking that text away in a 17th century format (i.e. the PDF of a journal paper today has much the same format and accessibility as a scanned copy of a journal article from hundreds of years ago).

In an attempt to bring scientific writing into the 21st century, a number of online LaTeX editors have begun to appear in recent years. An obvious advantage to online editing is that you don’t need to have LaTeX installed on your machine, however since installation is both free and relatively straightforward, this hardly represents a compelling reason for scientists to change the way they write. Instead, it’s the opportunity for collaboration and sharing that has the science community so excited about online LaTeX editing.

Online LaTeX editing is an area that many people are trying to innovate in at the moment (I came across a number of “sorry we’re shutting down because we couldn’t make any money” posts in researching this article), however the two editors that have gained the most traction are ShareLaTeX and writeLaTeX. In a nutshell, these editors are to LaTeX what Google Docs is to WYSIWYG editors like Word and OpenOffice. External collaborators can view and edit the document and there are comment and chat features for discussing changes. They also provide a kind of WYSIWYG functionality, as the PDF output can be generated alongside the text editor as you type. While this is an exciting step forward, the end result for a document on ShareLaTeX and writeLaTeX is still a PDF that locks away the text in that familiar 17th century (and not to mention proprietary) format. To fully exploit the advantages of the web, a different model is clearly needed.

Alberto Pepe and his co-founder Nathan Jenkins might just be on the way to establishing that new 21st century model for scientific writing and publishing. At the most basic level, their new website Authorea offers most of the features that ShareLaTeX and writeLaTeX do in terms of collaborative editing and commenting. In fact, their referencing (just put in a DOI and it figures out the rest), backup (you can link to your GitHub account instead of just DropBox), PDF export (pick a journal and it will format accordingly) and IPython notebook (you can include the code that was used to generate your figures – see here for an example) functionality represents a step forward on their competitors. At a higher level, Authorea provides a way forward from that 17th century publishing format. While it does allow authors to export to PDF, the most novel thing about Authorea is that it complies your LaTeX text (or Markdown, which may be the future of scholarly writing – see here) to HTML. Instead locking your text away in a proprietary format, Authorea makes it available on the web for anyone to view and comment on.

Linked my #PhD thesis on @authorea to my @github account - very cool. Just have to write the thesis now... @openscience @dfflanders @tjdett

— Damien Irving (@DrClimate)

April 10, 2014

One of the most exciting advances in scientific publishing in the last few years has been the rise of pre-print servers like arXiv. Since there is such a long time-lapse between when authors submit a manuscript and when the work is finally published, scientists are posting their work (in PDF format) to a pre-print server as soon as it’s done, so that the wider community can read their work while it’s being reviewed. In a recent interview, Nathan revealed that is “crazy long-term dream” is to fundamentally change the way that pre-publishing works. His hope is that people will pre-publish with Authorea instead, whereby their article is available in HTML format and people can comment directly on different sections of the text. This model is essentially a mix between old-school PDF journal articles and new-age blog posts, which is why there’s so much buzz around Authorea at the moment (e.g. see reviews on AppStorm and AppVita).

I recently created an account for my PhD thesis, so why not give Authorea a try for your next journal paper or manuscript?

[thestreamagazine-blog-blog]

STREAM PER CHE FUTURO!

La nuova scienza è una narrazione aperta, grazie ad Authorea.

Il 12 ottobre è uscito il nostro nuovo articolo per Che Futuro!

Questa volta, abbiamo parlato di Open Science e di narrazioni aperte, nel segno del remix e della partecipazione cre-attiva.

L'articolo completo, lo trovate qui.

[ushf]

Penflip: another entrant into the "Git for writers" market

Penflip is a similar concept to Authorea, which I noted earlier.  I don't quite see what's different, yet.  Discussion on news.ycombinator too.

There's nothing actually to see there yet, but the author has some good discussion of, and links to, the problems and opportunities in this area.