VanGorp2011ElsevierChallenge: SHARE - a web portal for creating and sharing executable research papers

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phvossen (5 years ago)

Fabulous! Congratulations! I hope to be able to use it soon for publication of my educational assessment tool PASS. PHVossen

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STOP AND ASK THE AUDIENCE: WHAT IS HE MISSING?

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Concerning AUTHOR, mention JETI etc. HERE!!!

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1. Please answer the following questions. How easy is it to answered question41  skipped question0 very easyquite easyquite hardvery hardCannot AnswerRatingAverageResponseCountset up a SHARE machine (as an author)?22.0% (9)48.8% (20)7.3% (3)0.0% (0)22.0% (9)1.8141access SHARE machines (as a reader)?61.5% (24)35.9% (14)2.6% (1)0.0% (0)0.0% (0)1.4139

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Pieter Van Gorp and Steffen Mazanek SHARE a web portal for creating and sharing executable research papers Procedia Computer Science, Volume 4, Proceedings of the International Conference on Computational Science, ICCS 2011, 2011, Pages 589-597, ISSN 1877-0509, DOI: 10.1016/j.procs.2011.04.062.

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The Bottom Line WHAT: SHARE is a portal for creating, running and publishing remote and secure virtual machines that contain all artifacts related to a research paper. PURPOSE: making computational research results reproducible for the upcoming decades SCOPE: anything related to complex software, competitive data sets, or both: software engineering, business process management, geo-sciences, bio-informatics statistical scripts (healthcare, ...) 2 WHAT: SHARE is a portal for creating, running and publishing remote and secure virtual machines that contain all artifacts related to a research paper. PURPOSE: making computational research results reproducible for the upcoming decades

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Overview 3

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Background: Organizing a Scientific Tool Contest 4

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SHARE An online platform for demonstrating research software Pieter Van Gorp http://w3.tue.nl/nl/diensten/bib/over/minisymposium/ 16/11/2009 “Research data! Who cares?” “Research software? We care!”

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First Discussion of SHARE (online: 5/2010) 6

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Overview 8

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Why something new? 9

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Example 1: STTT remote services (jETI) 10 Problems: High effort for Author (writing wrappers) Worst of all: Result = handicapped demo http://everystockphoto.com/ SHARE enables creation of uncompromised demos without extra coding

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Example 2: SCP Open Source, Fully Documented Installation, Configuration, ... “In physics or chemistry papers about experiments contain a lot of technical details in order to facilitate other researchers to replay the experiments in order to validate the results described in these papers” “More and more computer scientists use the Open Source community to distribute their tools. In this way it is not necessary to reimplement tools, only to download and install them.” M.G.J. van den Brand. Guest editor's introduction: Experimental software and toolkits (EST). Science of Computer Programming, 69(1-3):1 2, 2007. 11

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In this way it is not necessary to reimplement tools, only to download and install them… So why something new?

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13 Effort Volume Editor: Workflow? Future proof result? SHARE saves time and worries

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Limitations of Open Source 14 Effort http://everystockphoto.com/ Requires re-building best-of-breed comm. sols Waste of research budget, missed commercial opportunity

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Demonstrating Software: Levels of Accessibility Not Accessible Accessible After Request Available Online, Manual Installation Available Online, Manual Configuration Available Online, Fully Configured Cloud Computing Everything from the browser (AJAX, Flash, ...) Virtualization Ad-hoc resource reservation 15 SHARE is a portal for creating, running and publishing remote and secure virtual machines that contain all artifacts related to a research paper.

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16 SHARE executable paper = Text + data + code + documentation + license (if any) + ... Everything from the browser (AJAX, Flash, ...) Virtualization Ad-hoc resource reservation

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Architecture (TODO: no numbers, only 1 user,) 17

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Overview 18

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Screenshots + Demo Key features 19

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SHARE, as currently used for TTC’11 20 http://is.ieis.tue.nl/staff/pvgorp/share/?page=LookupImage&bNameSearch=ttc11

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SHARE: Typical User Walkthrough Reader/Reviewer walk-through Live demo: Configure new session for XP-TUe_BPMN.vdi Live DEMO

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Backup Starting sessions: 2:10 in http://www.screenr.com/T7K [offline MP4] Working remotely: 4:00 in same screencast. 22

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Collaboration: Image Cloning Core feature 23

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Cloning 24

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Backup choosing a base image and starting a machine for the cloned image. 1:40 in http://www.screenr.com/HWm [offline MP4] downloading/installing new software and publishing (or descarding) the result. 0:00 and 2:00 in http://www.screenr.com/WWm [offline MP4] 25

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Becoming a demonstrator... 26 Live demo: Request clone of Ubuntu 8.10 base

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Volume Editor, Host Admin, ... Administrative Features 27

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Organizer support in 2009 E-Mail from SHARE olaf.muliawan@ua.ac.be has requested access to bundle GraBaTs09.  To approve this request, please click on http://is.tm.tue.nl/staff/pvgorp/share/?page=ApproveBundleAccess&bundle=3&user=12&auth=48f3900475f43c984ff58fd6a0f5f0a2&approve=yes .  If you want to deny this request, please click on http://is.tm.tue.nl/staff/pvgorp/share/?page=ApproveBundleAccess&bundle=3&user=12&auth=48f3900475f43c984ff58fd6a0f5f0a2&approve=no . 28

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29 OK in the small, but was becoming a burden for the organizers...

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New (since last week...) Authors & Volume Editors add metadata 30 Live demo: Author update of metadata for XP-TUe_BPMN_i.vdi Better support for the publishing workflow!

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Typical meta-data: abstract etc., link to publisher website, link to screencasts 31 screenr.com, screencast.com, ... For true self-containedness: include MP4 in VM!

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Volume Editor (continued) Possible live demo of workflow for signup requests organizer updates to metadata lists, RSS: see list of TTC’11 accepted submissions and automatic index page with all TTC´11 papers Community artifacts: Template for the notification of acceptance for a SHARE-supported scientific event Sufficient documentation 32

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SHARE in social media 33

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@SHAREdemos: automatic notifications Synced via TwitterFeed service, inspiring example for volume editors 34

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Overview 35

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Current Applications (excluding my demos!) Research Events GraBaTs 2008, special issue in STTT journal GraBaTs 2009 Pre-Workshop proceedings Results of on-site activities (live programming contest) TTC 2010: All results of live contest finalized DURING workshop! LWC 2011, TTC 2011: lists & searches Research Demo’s PROM plugins, YAWL 2 (Ph.D. Thesis), ... Teaching MoDELS’10 => IM Master Thesis 36

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Usage Data (excluding anonymous user and myself) 37

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Latest News Extra VM server in 3TU-DC Availability, Durability Online survey: Preview Results Surprize for die-hard geeks who discuss research in bars, on the train, ...  38

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Q1: Ease of Use 39

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Q2: Confidence (as author) 40

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Q3: Confidence (as reviewer) 41

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Q4: Remote Virtual Machine Performance 42 Based on ≤ dual quad core 2.66Ghz ≤ 16 Gb ram

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Q5: Relevance of New Features 43

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Q6: Confidence (relation to SHARE host/sponsor) 44

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Q7: Open remarks By using Share, the review process of scientific papers will boost trust in the scientific community and it will motivate a better understanding of research works. Moreover, it will stimulate innovation, discussion and more collaboration between researchers. SHARE is an exellent tool for reviewers! The screencasts are an excellent compliment to the textual documentation. A conceptual overview diagram might be a useful addition too. More people should use SHARE to make their work reproducible! Please conquer the world.   When a system like share would be supported by a large publisher, e.g., if the share image would be accessible via the papers summary page (paper's DOI), this would immensely increase my confidence in the scientific system Point for improvement: RDP Applet 45

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Overview 46

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Keys to Success Enabler: Hypervisors have become commodity Huge investments by many businesses SHARE avoids “NIH” syndrome Great value for reviewers/readers: No Compromises Ideal installation Marginal additional effort for Authors that wish to `backup´ their results No more excuses... Not SHAREing = suspicious! Positive peer pressure 47

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Conclusions Executability: 5 Short and long term compatibility: 4 Validation: 4.5 Systems: 5 Size: 5 Provenance: 4.5 Other issues: risks and liabilities, security, viruses and code contamination, plagiarism, and other problems: 4 Feasibility – Is implementation possible overall and is it possible to implement on a publishing platform: 4.5 (even better WF support) Vision: 4 (many options: usage feedback to authors, survey 2.0, …) Generality/scope  with regard to scaling across disciplines: 3.5 NEW: support for huge files Will be evaluated by 3TU collegues (coast line analysis) 48

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Surprize…

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Platform support: SHARE on iOS  actually, makes a lot of sense! 50 Question: what is this?

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Backup: Systematic Related Work Overview 51 Source

Summary: Presentation for http://www.executablepapers.com/finalists.html, relates to research paper for the International Conference on Computational Science (ICCS 2011): http://dx.doi.org/10.1016/j.procs.2011.04.062

Tags: reproducible "research 2.0" virtualization cloud

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