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Jupyter and IPython facilitating open access and reproducible research

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the for and I go by many many many many phonemes Benjamin that I go when tried to get X of i am I'm in work on the other hand if the products are currently based in Oslo Norway at similar research lab which is a uh a small research laboratory that does work in biomedical computing and and commuters
systems and so we work on specifically in my group work on improving tools for science in general and in particular these Jupiter and IPython project what measures agree Jack and who cares knows what Jupiter is can go
here uses Jupiter on a regular basis in but the and who knows about the relationship of Jupiter and the hopefully everybody will know all those things that bad from the start
of with just a bit of of context about and how we do countries or research so my background is in computational plasma physics that in computer simulations of the plasmas and on mathematical models of that and coming up with the physical scaling laws and and things and this is from you know of our experience most of the suffer developers on that path
Indupa projects are assessed on scientist by training and physicists biologists and and the fact that the code over the sometimes reflects the fact that we're not the we haven't been suffer engineers although we've learned a lot of over the years so what's our process of doing computational research is served by the way I write some codes to around as described in whatever system I'm I'm interested in let I run that tho they think it's some results in and OK not that's a great results and actually can because of the 1 some figures to illustrate those those results that that that have up with 1 OK figure circle
interesting washes with the world so I write a paper and then published paper and and the people see it OK yeah that's interesting wanna reproduce that and then produce derivative works it's nice very nice clean
and linear process but in reality know it's a much more iterative process where now you write code you write it never works the 1st time in you you go back to change it and then of the get actual result in its in figures you do planning then you realize with those figures don't make any sense if good done something wrong and then you go back and change it and free run at OK now you think you've actually lecture finally got something together you write the paper then the review of yourself well know what I think maybe maybe need to re-run simulation with these parameters 1 see the sense of sensitivity these things or I don't trust your result please you know so that not much more substantially in in some way or another and then eventually you get to publishing the results and then even after the publication process you know
errors can get through the peer-review process we can end up going back and uh through the iteration even after the final product the the allegedly found by the other papers produced so far where
do where does our work fit into this so that Python started out as a way to solve this 1 little piece but we spend a lot of our time man In this process of our own figure out what could I wanna write or on its and and based on that running it had was figure out what it actually should have been published yet with an expert inclination right and so 1 and was
developed by a friend presence as a PhD student at the too bad that helps a process and learning the code for a for his research so what is I want the eyes for enacted it's just the environment for the better interactive Python with the focus on this the kind of work that scientists do
of of flooding and making them interrogating code so that the 1st thing it does is found give you things like that completion so you can say know I know when he's this package and I wanna do something and
related to erase applauding the antenna and lesion you more easily find that without having to refer to the documentation as much has introspection so this is in addition to the Python language we can say OK I and only use this a momentary that object is it how can I use this and and that's another way to more quickly figure out and if people are familiar with libraries like matplotlib and then there's a lot of these tools have very very complicated and signatures and can you kept either spend a lot of time the documentation we can quickly peak not the doc strings of these of these objects to say and they had promised was to use this in the which argued what's the argument order and things we can really quickly look up that information in an interactive session effect by them last thing we do are these magic so that our extension of the extension to the Python language 4 shell like syntax more efficiently things like I'm running timers changing working directory simple things to make that interactive shell experience of bit more pleasant than than plain Python to so that's where my preferences on so that Jupiter and Jupiter that head is a bit more ambitious uh where we want to use that as we develop a scientists and expand the project
1 kind of work on as the some degree every every piece of of this problem but so what is Jupiter but there are a lot of answers this question and to give a few of them at the 1st level and this is an answer that most people may be unaware of Jupiter's is
a protocol so it's a and we talked about I Python is a shell where you're running code interactively and the 1st thing we build that that ultimately became Jupiter's was built in the IPython and project of originally as just a technical feature of I want and we want weird where you could actually
executes and then the user interface and that's presented to you to be separate of 1 of the reasons for this is if you have in this code often near your any guessing running code in C or Fortran that's called from Python and that code can all can fail in more dramatic ways than than Python confess attempted on the processing you can lose everything and it would be nice if you didn't lose your at the application the interface
as well you know you might and lose the runtime state of of the code that we'd like to to keep their the persistent and so and that and some other reasons we need uh broke this protocol that OK when we do an IPython this on this process of reading code executing increasing output and we defined protocol for that so that we could separated the user-interface from the execution the but you but also defines a
document from so this is a a Jupiter notebook which contains the mathematics and frozen and code and the out with that's the results from an act of novel and more detail of that are in a bit but we have these 2 or these 2 really basic technologies of a given a book is a document that format and and the Jupiter protocol that we use for execution so a bit of detail but there the
protocol so at its the protocol consulates appeared we call at a
redevelopment which is how the shells in the terminal working on In the 1st step is read which is fast asked it get some input for what code to run and and this is this traces of a message that those to the front ends and the message for the next you request the is the code that you wants to run as text
and then the evil is a so that the process that we call the kernel which is the a question is OK and then run that code do whatever that code says to do and the that where
we depart from the terminals of that is the price that where in because we're sending these messages we can send out outputs that not just text were not too for not confined to a terminal we can produce outputs and that can be a variety of types and we identify these types by mime type and which is the way the when identified what kind of document itself and if you view web page it's going to be a cynic idea Nacional documentary B you can also view and other types of
files on the web images and things and we use the same concepts to identify what kind of outputs that are produced uh then the weekend that same information the browser which ends up ultimately displays and the
loop is just you is over and over again in next session you just taking that's a Kodiak Eckstein and you looking at the results the so bit about that that extended peak printing the in the rebel and we use mine that's for output which means that we can any any format of of a file or others but from their weakened values into so that the basic output but is text and that's that simple and
you just got some some tax outputs that we wanted to see that text and you can display so here's a a bit of code that produces some some simple text because of images so this is a commonly
used ones plotting in relation it produces simple roster vector that indigenous CG European G we
can also have outputs that is itself a lotic mathematics so we have and in the book of for example we render the we render in mathematics in the in the browser using a library called laughter the same thing that runs on on archive catalog invasive sites that that render at and the the output of the of of this expression is not the and not the relevant it's not really about not image the output is actually on the lot tech expressions and then that the browsers possible for rendering and the nice thing about that is that different consumers of this notebook can render the plot that as appropriate in different environments need on not stuck with some rendering that that you have to include as as an image of an
embedding into something else we can also have an output that is itself issue of a script and this is where a lot of the power of
the the when they well the lies he can have on fully inactivation known and JavaScript outputs and this is a simple table on Beacon House outputs to do what they can do on web page you can do is not put in a and and last thing you can have an output that is itself actually in input so this is a an inactive would you wear and by the output of this execution is actually a control that when you move uh the slider in this case it actually executes the cell and produces an output so this is interacting with a factoring out of an equation is and as you just move this this is factor yes the n minus 1 and as you move the slider changes and but and then recomputes the result the the and then and this is key to
the protocol we talk about polling the execution that apart from of the interface and the way we did that with the outputs seduced he by mime type the of the input is just the code as text behind Python-specific about we wrote this we did it this way for IPython because we wanted you know we want to use is Python in this way but kind accident
of we we made this in such a way that would be useful to any interpreted language and so we know we document the protocol this is how it works end of their language communities have adopted that there are now
currently and I believe just over 80 kernels for Jupiter and in languages from C + + and uh to to JavaScript in Erlang and and and various kernels for spot can all our and so that that you juvenile model can be used as a in a in a variety of ways with a variety of language you know set was and if that's the language choice so a bit more detail about how
would a new book is so at the most basic level in a book is a sequence of cells so there are 2 kinds of cells that text cell contains marked down I'm and lot that mathematics and this is rendered on the browser and a code cell is 1 of these redevelopment so it's the code you execute and then it also includes the output that's produced so that the cell contains in the output of of an execution in and then there's the others metadata everywhere for of marking marking these things up that can be used for consumers of books the file format and is a plain text data format that is bound uh publicly documented schema so it's found if all the Jupiter suffered goes away you can still take your notebooks and easily get uh get your code and output uh out its machine readable because it's a very simple Jason data structure and that's easy to understand the poking around with a notebook so if you have a decent portion is is pretty simple but and because of the structure of the documents that the document is not this each cannot harm the document is a simple data structure of you can take
that structure and transformants to a variety of other formats you can turn it into a binational document you can turn
into a lot like document you can turn it into marked down for some blogging engine and and then you can also provide a custom converters to take a notebook and convert it to to any format and because of this simple scheme of of of notebook it's as it is not too difficult to write
transformers for the folks to integrate into an existing publication pipeline the that's the book as as a document of the new book is also the inactive environment so be the this where patient but where you actually create of books i is an inactive computing environment for kind of data exploration and then put your poking around the data for learning and and exploring and I would send an
imprisonment books and once a prison of would also be input format to but once you can say again this notebook it's that some of this info them and some results I want to and I want to point this notebook into some competition pipeline and produce a reporter and notebook or something all men do offline execution and the books and be an output format so that you can have some big offline simulation of that automatically programmatically produces an output document to enable interactive exploration was that with your results and so the way this
fits and for us the way this fits into that of the of
open science and reproducible research where area is so you start out with in France in the interactive and model
where you're just exploring you know because of interactive scratch the environment can poke around learn figure we wanna do and find something interesting and then from a sustainable software perspective on so you're learning in the notebook and then you producing suffer as you normally would you know you not writing your suffer in the notebook and your writing your software and this the same way you produce any an any good library and many use that library again of the the the and then once you've got something complete that works you have perform analysis you run your simulations you and you do as a sum exploratory work and actually producing something I a collaborative analysts with your peers and in you know books that actually illustrate how we're interested and then I so they've actually done then you work you got interesting results and it's time to communicate with the outside world the and no books are a really nice way for communicating computational ideas of saying thing here is in my mark on my math you
this is what I'm doing this this is my mathematical model the below that you have the code implementing a mathematical model from and then you have the more you have the figures illustrating results and and then you can share that an both as an HTML file that people can uh view and but also because it is the document that is all is act violent people can download that notebook and run it and change it but actually use that and to explore and interact with your results without having to from search server scratch and
then work additional publication contexts and output can be used as a people as part of the term computational companions and for the provision papers so there a number of at the publications using books as appendices or and kind of companion things like this is in a book that generates every
figure in this paper on or this is another but actually goes through and the analysis of that implements this entire model it so people can say that the EM images in this traditional paper of highway start interacting with that it's a confusion a book you can just you can uh I've got head and can interact with others and produced so a
couple of the applications of of Jupiter we have the Jupiter lab is a new a new web application for interacting with but with Cuban of books and and other things and there's any converter is our tool for picking the books and converting them to additional on marked down a lot that can be a the and B viewer which all demonstrate shortly and is a service that basically any convert on the let where you you point as with other governments as basically any public notebook you can render that Taichung armchair and Juba hub is a tool for the hosting kept computational resources in giving this is focused on the interactive side of giving at giving people access to uh
uh uh computational resources through through no books and be greater is a tool other works with uh Jupiter called for automatic grading and and uh assignment dissemination event and turning assignments automatic validation and and upgrading of of notebooks as academic assignments so I can then be is service for demonstrating running of the small scale of free hosted computing a notebook by using doctor and the B at so we talked about the protocol a document format yet you have so we don't have to use on the entire Jupiter stack all at once and you can just use the protocol and for remote execution of and
get all the power of the execution splayed Jupiter without using notebooks and the use of example that of turning any little code blocks on a page into the uh could be you can execute and without there being any notebooks involved the thickness say OK I wanna run this little block of code that's on this webpage me on blogger something as something from O'Reilly's erase it on their web pages you can execute this code and see the results and without
the actually beginning books involved and the radius of other examples of of tools and and different using different pieces and different combinations of of the perspective build different different application some are purely not purely document focused on popular execution focus and some use the whole thing together so
this is mentioned in Gedaliah it'll go a little bit more in depth and so 1 of
uh 1 good example we have of Jupiter in in science and it's the like go to Paris so this is a direct observation of of gravitational waves and with the bigger leap that laser uh in a Frommer's and and what they did was the of like you know which is a massive collaborative physics experiment but has something called the light go Open Science Center I'm making this
go here but and the like Open Science and there is a whole other a piece of the
look the lego experiment that's devoted to the making of the the scientific results that they produce at like go
available to the wider community and 1 of the ways they do that and is when they have a result and they produce these about juvenile books that explain and how
to go through and say consist of the thickness of quick velar so you know
and but this and they publish these notebooks that are tutorials for how to actually download the
like data the through the analysis and download you know so for this direct observation of gravitational wave you can download this notebook and and and run it and will actually get the the actual data that they use good the actual simulation since actual analysis that they that they ran and and Dennis and show how they came to the conclusion that they came to the and 1 of the uh the coolest
pieces of this is the he services and so Microsoft Azure and other metadata about service allows running an of
books on on the uh uh cloud systems of an accountant is also a serviceable binder and that's a a free service that any new books by put on get help with some a declaration of their of the requirements you can so this is the URL and you'll get a temporal container with the dependencies in you can actually run on these notebooks there's this of the venture strain of people are working on some of the uh the guns and and and intelligent but on that so
solution so this is the thing now but the I would buy here this is extremely useful for these these kind of open science applications of the tying together of public nature data available on in the making of what's available lenders currently tied to get and that it is it has to be the end then people can just click a link and the got an interactive execution environment with a document explaining what's interesting and that they can actually executed follow along and of modifying produced drive things from from your scientific results and
actually in interact with some wonderful to executable environment then the that's
about to cover yeah the the
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Metadaten

Formale Metadaten

Titel Jupyter and IPython facilitating open access and reproducible research
Serientitel 2nd Conference on Non-Textual Information: Software and Services for Science (S3), May 10-11, 2017 in Hannover
Teil 11
Anzahl der Teile 13
Autor Ragan-Kelley, Benjamin
Lizenz CC-Namensnennung 3.0 Deutschland:
Sie dürfen das Werk bzw. den Inhalt zu jedem legalen Zweck nutzen, verändern und in unveränderter oder veränderter Form vervielfältigen, verbreiten und öffentlich zugänglich machen, sofern Sie den Namen des Autors/Rechteinhabers in der von ihm festgelegten Weise nennen.
DOI 10.5446/31024
Herausgeber Technische Informationsbibliothek (TIB)
Erscheinungsjahr 2017
Sprache Englisch

Inhaltliche Metadaten

Fachgebiet Informatik
Abstract Jupyter notebooks provide a document-based interactive environment for performing and recording computation. Notebook documents contain not only the code that is run, but prose and mathematics for describing the analysis, as well as recording the outputs of the computation, from plain text output to rich interactive media, such as HTML and javascript or images and video. Jupyter notebooks are being deployed widely as computational companions for publications, facilitation reproduction of results, and interactive exploration and modification of analyses, including by prominent scientific discoveries such as the LIGO experiment. Being freely available, open source software, Jupyter and IPython aim to improve the accessibility of reproducible practices in computational science.

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