Michael Zingale is a computational astrophysicist who enjoys blowing up stars and working on new algorithms to enable these simulations.  He is an Associate Professor of Physics and Astronomy at Stony Brook University on Long Island, NY.

Many of us have written notes for our classes or have searched online for notes written by our colleagues that we can use in our classes.  To help coordinate the effort of sharing and building texts for astrophysics topics, I started a github organization called the Open Astrophysics Bookshelf:

http://open-astrophysics-bookshelf.github.io/

The basic idea is that we, as a community, can crowdsource texts on astrophysics topics and make these freely available (via the Creative Commons license) for anyone to use.  And since we tend to use LaTeX for our scientific writing, these texts can be easily managed by git version control.

Essentially, the Open Astro Bookshelf is just a github (http://github.com) organization where different texts can be hosted as git repos.  There are two cases one can imagine for adding to the bookshelf.

  1. Many of us have our own set of notes (or a draft text) on a topic in our area of expertise, with varying degrees of polish.  In this case, you are starting off with something that is already substantially developed.  By hosting this text on the Open Astro Bookshelf, you gain input from the community—people can contribute changes via github pull requests.  These can be anything from typos, requests for clarification, figures, or entire chapters.  Since the work is hosted on github, all contributions will be noted in the git log, but a project can also include an author list noting the primary author, major contributors, other contributions, etc.
  2. There are some topics that we all know are in need of a good up-to-date text, for instance, to train students in techniques of our trade.  A Scientific Computing Cookbook is an example.  (Another idea suggested by a colleague is an AST 101 text).  In this case, we can start a text in a repo that is a stub, simply an outline, and rely on crowdsourcing to write the text from scratch.

Since everything is openly licensed, anyone can create mash-ups of the content to suit their needs.

In contrast to traditional books that go through a publisher, these texts are living.  They can continually be updated.  But don’t worry—we can still cite an “edition” via the git hash (it is quite straightforward to have a makefile put the git hash into the LaTeX source at compile time).

There are already some examples of each of the above cases up online.

I’ve moved my set of notes on Computational Astrophysical Hydrodynamics there, Mark Krumholz has put up his notes on Star Formation, and Ed Brown has contribute his Stellar Physics notes.  I’ve reached out to others in the field who have expressed interest in putting up their notes as well, so I hope for this to grow  quickly (especially now that it is summer).  I’d like to encourage anyone else who is interested to contact me, and we can setup a repo for your notes as well.

There is also an mostly empty template for a Scientific Computing Cookbook to share tips/techniques and good practices across our field—this latter one is a case where crowdsourcing can hopefully put something nice together.  This idea arose from discussions I’ve had with many of our computational astrophysics colleagues, and I’m told that a similar idea has surfaced among the astrobetter community.

As this is all new, there is still a lot to learn about how to best coordinate the different efforts.  I think that each text needs a lead (or leaders)—they set the tone of the text, make the initial organization issues, and will have the admin access to merge pull requests.  The number of people in this role can evolve with time as people become bigger contributors.  Anyone else in the community can interact via the normal github mechanism—pull requests and issues.

I’ve setup a mailing list to discuss these ideas as well:

open-astro-books@googlegroups.com

(you can subscribe here: https://groups.google.com/forum/#!forum/open-astro-books )

Please don’t hesitate to contribute.  There is a lot of potential for us to build up a bookshelf that covers a wide range of topics in our field, that is freely available to everyone (students certainly don’t like paying for books), and is continually brought up to date.

What texts do you think are needed?

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ADSBumblebeeAlberto Accomazzi (@aaccomazzi) is the Program Manager of the NASA Astrophysics Data System based at the Harvard-Smithsonian Center for Astrophysics.

The Astrophysics Data System (ADS) is a tool for finding astronomy and planetary science publications. ADS currently has three different interfaces:

  1. ADS “Classic” — the one you all know and love,
  2. ADS “Labs” or “2.0” — the first interface to an updated search engine, and
  3. ADS “Bumblebee” — currently under active development.

We are very pleased to introduce Bumblebee! This interface is in the beta stage of development and is ready for more users. It features a clean look and powerful search and filtering operations but it is indeed a beta and still has some quirks and bugs. However, there are some features which we think you’ll find so useful, we want to tell you about them as soon as possible. Over the next couple months, we plan to highlight some of these features in a series of blog posts, so stay tuned!

The search engine that powers  Bumblebee enables faster and more complex searches than Classic. Classic is well suited for things like finding articles by author or title, but it lacks the ability to examine citations, search full-text, or progressively filter results.  We are incorporating all of the features found in Labs and Classic into Bumblebee and are anticipating that Labs will be deprecated and replaced by Bumblebee by the end of 2015.

Never fear, ADS Classic will remain available and supported for the foreseeable future. However, while bug fixes are being applied, Classic is not undergoing any new development. In the very far distant future, long after you and your postdocs have retired, when Classic is deprecated, all abstract page URLs will remain fully functional and so there will be no broken links and no need to change your links to ADS.

The myADS notification service will remain unchanged for the moment. In the next year or so we expect to provide an even better custom notification service using the same technology which underpins Bumblebee.

If you want to be on the bleeding edge and help us run Bumblebee through the paces, please check out the Help Pages for instructions on how to search and give it a go. We welcome your feedback on Bumblebee via issues on the Github repo, tweets to @adsabs, or email to adshelp@cfa.harvard.edu.

All of Bumblebee’s code is publically accessible on Github and issues and pull requests are always welcome. The API powering Bumblebee is also available to users and we are planning to publish the documentation for it soon. If you would like to develop widgets or applications to interface with ADS services, you can generate an API Key by creating an account and navigating to the API Token section in Settings. We are looking forward to future hack days and seeing what the community builds with these services!

Questions or comments about these ADS services? Let us know in the comments!

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Matteo Cantiello is a theoretical astrophysicist at the Kavli Institute for Theoretical Physics and Authorea’s Chief Scientist.

I am aware that a while back a lot of astronomers have tried out writing their research articles on Authorea, a web-based collaborative writing platform. Some were disappointed by the lack of certain advanced LaTeX features (e.g., deluxetables, now supported). You were disappointed, you told us why, and we just implemented some big changes to make you happy. Authorea now has a ”Power LaTeX user” mode which supports a much much larger subset of LaTeX. Essentially everything. And unlike some services such as ScribTeX and WriteLaTeX (previously reviewed on Astrobetter), all your LaTeX renders both to PDF and to HTML (i.e., the web).

So, why should you give Authorea a spin and start using it daily for your research? It’s a good question. Here some highlights that might guide that decision.

  1. 1.With Authorea, your paper is accessible from any computer, anywhere in the world.
  2. 2.You can write your paper from your browser, no installation of TeX required.
  3. 3.You can write in LaTeX or in markdown. Advanced LaTeX and tables are now supported.
  4. 4.Collaboration is made easy. No need for endless emails threads with multiple draft revisions.
  5. 5.Every Authorea paper is a Git repo, version controlled. Again, no installations required.
  6. 6.Want to work offline via Github? You can. Authorea becomes the rendered version so that your coauthors can still work with you without having to learn Git.
  7. 7.Adding citations has never been easier. One click and done. Believe me, you will never want to go back.
  8. 8.You can include data and code in your paper, like IPython Notebooks. This allows for transparency and reproducibility of results.
  9. 9.Export to any journal format with just one click. We support all the usual suspects, from ApJ to AJ, from MNRAS to A&A. Switch back and forth between these styles in one click.
  10. 10.Powerful commenting system. For internal or even external review.
  11. 11.Authorea has templates to get you started fast with your next Astronomy grant proposal or d3.js paper.
  12. 12.Did I say deluxetables? Well, here’s the same deluxetable posted on Astrobetter a while back, as it is rendered on Authorea: https://www.authorea.com/38778_deluxe.

Ok, enough with the list of fancy features. Here’s my personal experience as an astrophysicist using Authorea. I switched to writing papers with Authorea about a year ago and I noticed a number of immediate improvements: first of all my papers get written faster. Then I noticed that I have no need to exchange emails with collaborators concerning the paper. All the action happens (and it’s logged) on Authorea, including discussions about revisions and suggestions for improvements.

This said, I didn’t really expect the most important upturn. By getting rid of the overhead I had previously considered a messy unavoidable part of the scientific writing process, something remarkable happened. I actually started enjoying writing more!

And I don’t mean just publishing; I had experienced that joy before. The difference is I now cherish the time I spend putting my science into words. It might sound crazy, but Authorea did something amazing: it made me discover the pleasure of writing science together with my collaborators.

So if you ask me ”Why should I write my next paper with Authorea?” my honest answer is ”Because you will love it!”. My suggestion is that you take Authorea for a spin and make up your own mind.

The Astronomical community has a lot of experience with early adoption and innovation, so your feedback can help to substantially improve this tool. Do you think Authorea is on the right track? Is there a particular feature missing that would improve substantially your workflow? Share your reviews and suggestions in the comments!

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Brian Kent is an associate scientist with the National Radio Astronomy Observatory working on pipeline software for VLA and ALMA, and has interests in galaxy surveys, dynamics, and 3D graphics and visualization.

A new book published by IOP is now available entitled “3D Scientific Visualization with Blender.” This work is written for a broad scientific audience of students and researchers interested in rendering their data in 3D. The book introduces the reader to the interface, how to build and manipulate 3D objects, animate a scene and render a result, and read data into models through the Python API. A chapter with simple examples concludes the book as a launching point for the reader to begin developing their own visualization and analysis scenes. A number of the examples are relevant to astronomical data analysis. The new book available through Amazon or IOP Publishing also has a companion website. The sample video tutorial below exhibits some of the ideas featured in the book.

In the age of large astronomical dataset, it is exciting to consider new software paradigms that might aid us in 3D visualization. Building upon these tutorials, what kinds of visualization scenarios can we envision?

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The Starchive: An open access, open source database of the nearest stars and beyond

by Guest April 27, 2015

Angelle Tanner is an assistant professor at Mississippi State University with interests in multiple methods of exoplanet detection and characterization. Situation 1:You make a preliminary list of target stars using SIMBAD and then follow up with a tedious search through Vizier and individual papers for all the additional observational data you need to motivate a […]

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Fabric Conference Posters FTW!

by Guest March 25, 2015

Emily Rice is an assistant professor at the College of Staten Island and a research associate at the American Museum of Natural History. She is also responsible for those parody songs that get stuck in your head. Dearest Colleagues, I have printed my last paper conference poster and carried my last poster tube. Forsooth I […]

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Details and discussion about impending changes to ApJ and AJ

by Kelle February 13, 2015

During AAS225 in Seattle, there was an announcement about changes coming to the AAS Journals: Astrophysical Journal (ApJ), Astrophysical Journal Letters (ApJL), and the Astronomical Journal (AJ). These changes include lots of awesome things such as “linking articles directly to data archives, providing for video abstracts, improving figure presentation, making figures interactive, introducing the ability […]

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Licensing Astrophysics Codes session at AAS 225: Link

by Danny Barringer February 4, 2015

For those of you not in the know, at the past AAS meeting, a session was held on Licensing Astrophysics Codes based on suggestions that such a session would be interesting and useful to astronomers. This is a topic previously discussed in an AstroBetter guest post by Jake VanderPlas in March of 2014. In case […]

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Data Exploration with Glue

by Guest February 2, 2015

Chris Beaumont is a software engineer at Counsyl, and previously a software engineer at Harvard and the Space Telescope Science Institute. Glue began as a side project during Chris’ PhD thesis, and is now being developed to visualize data from the James Webb Space Telescope. We’ve recently released version 0.4 of Glue, a Python-based GUI […]

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Using WriteLaTeX for Collaborative Papers

by Guest January 12, 2015

Adric Riedel is a postdoctoral researcher at the College of Staten Island, working with the Brown Dwarf research in NYC (BDNYC)  group. We all love Google Docs. It’s a functional and convenient way to share and collaboratively edit documents across platforms, time zones, and even continents. We in the BDNYC group use it extensively. But […]

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