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Research	So+ware	and	Science	Gateways:		
Addressing	Sustainability,	Usability	and	
Reproducibility	Challenges	to	Enhance	R...
2	
• 	In	the	middle	of	nowhere	of	northern	Indiana		
	(1.5	h	from	Chicago)	
• 	4	undergraduate	colleges		
• 	~35	research	...
• 	So+ware	development	and	profiling	
• 	Cyberinfrastructure/science	gateway	development	
• 	ComputaHonal	ScienHst	support	...
So+ware	Sustainability	
Sustainable	so+ware	is	so+ware	which	is:	
•  Easy	to	evolve	and	maintain	
•  Fulfils	its	intent	ove...
So+ware	Sustainability	
h_ps://www.so+ware.ac.uk/about
Sustainability	for	Cyberinfrastructure	-	NSF	
	
	
	
	
SI2	
So+ware	Infrastructure	for		
Sustained	innovaHon	
CSSI	
Cyberin...
Sustainability	for	Cyberinfrastructure	-	NSF	
Sustainability	InsHtutes	and	Excellence	Hubs	are	
funded	to	support	the	CI	a...
Research	So+ware	
h_p://doi.org/10.5281/zenodo.843607
Research	So+ware	
h_p://doi.org/10.5281/zenodo.843607	
>	50%	neither	formal	nor	informal	training		
in	so+ware	engineering
Research	So+ware	
h_p://doi.org/10.5281/zenodo.843607	
Lack	of	career	paths
Research	So+ware	
h_p://doi.org/10.5281/zenodo.843607	
How	to	cite	so+ware?
Areas	of	Concern		
	
•  FuncHoning	of	the	individual	and	team	
•  FuncHoning	of	the	research	so+ware	
•  FuncHoning	of	the...
FuncHoning	of	the	Individual	and	Team	
•  Training	&	educaHon	
•  Ensuring	appropriate	credit	for	so+ware	
development	
• ...
FuncHoning	of	Research	So+ware	
•  SupporHng	sustainability	of	the	so+ware	
•  Growing	community,	evolving	governance,	and...
FuncHoning	of	the	Research	Field	Itself	
•  Growing	communiHes	around	research	so+ware	
and	disparate	user	requirements	
•...
URSSI	and	Other	S2I2	Projects
URSSI	and	Other	S2I2	Projects	
Goal:	Close	collabora-on	and		
fill	in	gaps	on	each	axis
Partner	with	URSSI	
We	don’t	want	to	reinvent	the	wheel	but	partner	
with	exisHng	iniHaHves!	
•  UK	SSI	
•  So+ware	and	da...
IniHal	Straw	Man
ConceptualizaHon	
•  Workshops	
•  First	workshop	took	place	in	April	in	Berkeley	
•  Second	workshop	took	place	in	Octobe...
How	to	Engage	with	URSSI	
•  Watch	the	website	h_p://urssi.us/	
•  Repos	for	website	and	workshops		
h_ps://github.com/si2...
Technology-Enhanced	Research	
22	
•  Increased	complexity	of	
•  today’s	research	quesHons	
•  hardware	and	so+ware	
•  sk...
23	
Data	and	compute-	
intensive	problems	
High-speed	networks	
Users	generally	not	
IT	specialists	
Tools	and	workflow	
en...
24	
Data	and	compute-	
intensive	problems	
High-speed	networks	Tools	and	workflow	
engines	
Web-based		
agile	frameworks	 D...
25	
Data	and	compute-	
intensive	problems	
High-speed	networks	Tools	and	workflow	
engines	
Web-based		
agile	frameworks	 D...
It’s	a	
Science	
Gateway	
It’s	a	
Research	
Portal	
It’s	a	
Collaboratory	
It’s	a	
Cyber-		
infrastructure	
It’s	
a	Virtua...
Science	Gateways	
Gateway	users	are	77%	of	acHve	
XSEDE	users	in	Q4	2016	
This	is	largely	due	to	the	CIPRES	and	I-TASSER	g...
Life	Cycle	of	a	Science	Gateway	
Developers	typically	
•	work	in	isolaHon	
•	must	bridge	to	
variety	of	resources	
•	need	...
Science	Gateway	Survey	2014	
30	
What	services		
would	be	helpful?	•  sent	out	to	29,000	persons	
•  4,957	responses	from	...
Science	Gateway	Survey	2014	
31	
34% 36%
20%
17%
31%
26%
42%
16%
30%
18%
45% 44%
14% 15%
0%
5%
10%
15%
20%
25%
30%
35%
40%...
32	
“A+er	all,	usability	really	just	means	that	making	sure	that	
something	works	well:	that	a	person	…	can	use	the	thing	...
Technologies	
•  Widely	used	complete	frameworks	(Galaxy,	HubZero,	Globus	Online	etc.)		
•  RESTful	APIs	and	support	of	mu...
Science	Gateways	Community	InsHtute
Sustainability	via	On-Campus	Teams	
On-campus	teams	
It	is	a	centralized	team	at	your	
insHtuHon	–	
irrespecHve	whether	yo...
Connect	with	SGCI	
Incubator	Sustainability	Bootcamp	
•  h_ps://sciencegateways.org/engage/bootcamp	
	
•  5	full	days	
•  ...
Connect	with	SGCI	
Incubator	Sustainability	Bootcamp	
•  h_ps://sciencegateways.org/engage/bootcamp	
Work	with	us	
•  h_ps...
Interagency	Workshop	2019		
	
	
Funding		
agencies	Contact:	
Nancy	Wilkins-
Diehr	
wilkinsn@sdsc.edu
Bridging the Gap to Data Sharing
Researchers
“the local academic community struggles to effectively manage its assets whic...
Current Lifecycle of Research Projects
Hesburgh	Libraries
SelecHon/	
development	
of	tools	
Data	
assembling/	
creaHng	
Re...
Target Lifecycle of Research Projects
Hesburgh	Libraries
SelecHon/	
development	
of	tools	
Data	
assembling/	
creaHng	
Rep...
PresQT
A	collaboraHve	design	effort	to	enhance	
reproducibility	and	more	open	sharing	of	
research	data	through	open	source...
Hesburgh	Libraries
h_p://presqt.crc.nd.edu/
Two Workshops & the
Needs Assessment
answered by 1740
stakeholders have been
c...
Hesburgh	Libraries
Collaborative Effort
Where	we	are	now
h_ps://osf.io/d3jx7/	 h_ps://cos.io/	
Project Partner
An open project with all
stakeholder input,
workshop materials, and
...
Needs Assessment Results – over 1700
answers
https://ndlib.github.io/PresQTNeeds/
Repository and Tool Agnostic Solutions
•  Open	design	of	tools	and	services	using	standards
•  Integrate	with	workflows,	to...
Open Design Document
•  Open	design	of	tools	and	services	using	standards
•  Integrate	with	workflows,	tools,	and	virtual	e...
Partners and Committed Collaborations
•  Sheridan	Libraries,	John	Hopkins	University	
•  NDS	
•  UC	San	Diego	Library	
•  ...
Partners and Committed Collaborations
•  Sheridan	Libraries,	John	Hopkins	University	
•  NDS	
•  UC	San	Diego	Library	
•  ...
Contact us: presqt-contact-list@nd.edu
PresQT on the web: https://presqt.crc.nd.edu/
Subscribe to our newsletter!
Hesburgh...
Thanks!	
		
sandra.gesing@nd.edu	
	
h_p://urssi.us	
h_ps://presqt.crc.nd.edu	
	
h_ps://sciencegateways.org/
URSSI - SGCI - PresQT: Research Software and Science Gateways:  Addressing Sustainability, Usability and Reproducibility C...
URSSI - SGCI - PresQT: Research Software and Science Gateways:  Addressing Sustainability, Usability and Reproducibility C...
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URSSI - SGCI - PresQT: Research Software and Science Gateways: Addressing Sustainability, Usability and Reproducibility Challenges to Enhance Research �

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Research software plays a major role in academia evident in the fast developing landscape of simulations and modeling and new evolving areas such as deep learning. Research software has been gaining increased attention in the last 5 years than ever before. Science gateways are a subgroup of research software addressing the needs for seamless end-to-end solutions so that scientists can focus on their research questions instead of becoming acquainted with details of the often complex underlying computing and data infrastructure. Providers of distributed computing infrastructures such as XSEDE report since 2013 that more users apply their resources for research via science gateways than via command line. Recognizing the importance of software and science gateways, the conceptualization of the US Research Software Sustainability Institute (URSSI) and the Science Gateways Community Institute (SGCI) that is funded since 2016, aim at addressing challenges to achieve sustainability of software and increase the usability of complex computational methods to accelerate research. A cornerstone of science is reproducibility and even though solutions such as science gateways support reproducibility of research, the current landscape needs further tools and concepts to address the reproducibility challenges. One of the goals of the project PresQT (Preservation Quality Tool) is to step into the gap to connect existing systems to achieve easier curation and preservation of data and software and thus, contribute essentially to reproducibility of research. The talk will go into detail for the research software and science gateways landscape in the US, challenges faced by projects and the actions and vision of URSSI, SGCI and PresQT.

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URSSI - SGCI - PresQT: Research Software and Science Gateways: Addressing Sustainability, Usability and Reproducibility Challenges to Enhance Research �

  1. 1. Research So+ware and Science Gateways: Addressing Sustainability, Usability and Reproducibility Challenges to Enhance Research Sandra Gesing sandra.gesing@nd.edu Webinar at NITRD Program’s So+ware ProducHvity, Sustainability, and Quality Interagency Working Group December 6, 2018
  2. 2. 2 •  In the middle of nowhere of northern Indiana (1.5 h from Chicago) •  4 undergraduate colleges •  ~35 research insHtutes and centers •  ~12,000 students University of Notre Dame
  3. 3. •  So+ware development and profiling •  Cyberinfrastructure/science gateway development •  ComputaHonal ScienHst support •  CollaboraHve research/ grant development •  System administraHon/ prototype architectures •  ComputaHonal resources: 25,000 cores+ •  Storage resources: 3 PB •  NaHonal resources (e.g., XSEDE) •  ~50 researchers, research programmers, HPC specialists CRC and OIT building h_p://crc.nd.edu CRC HPC Center (old Union StaHon) Center for Research CompuHng
  4. 4. So+ware Sustainability Sustainable so+ware is so+ware which is: •  Easy to evolve and maintain •  Fulfils its intent over Hme •  Survives uncertainty •  Supports relevant concerns (PoliHcal, Economic, Social, Technical, Legal, Environmental) (Patricia Lago at WSSSPE4)
  5. 5. So+ware Sustainability h_ps://www.so+ware.ac.uk/about
  6. 6. Sustainability for Cyberinfrastructure - NSF SI2 So+ware Infrastructure for Sustained innovaHon CSSI Cyberinfrastructure for Sustained ScienHfic InnovaHon
  7. 7. Sustainability for Cyberinfrastructure - NSF Sustainability InsHtutes and Excellence Hubs are funded to support the CI and research community ConceptualizaHons •  US Research So+ware Sustainability InsHtute (URSSI) •  GeospaHal •  … ImplementaHons •  Science Gateways Community InsHtute (SGCI) •  The Molecular Sciences So+ware InsHtute (MolSSI) •  InsHtute for Research and InnovaHon in So+ware for High Energy Physics (IRIS-HEP)
  8. 8. Research So+ware h_p://doi.org/10.5281/zenodo.843607
  9. 9. Research So+ware h_p://doi.org/10.5281/zenodo.843607 > 50% neither formal nor informal training in so+ware engineering
  10. 10. Research So+ware h_p://doi.org/10.5281/zenodo.843607 Lack of career paths
  11. 11. Research So+ware h_p://doi.org/10.5281/zenodo.843607 How to cite so+ware?
  12. 12. Areas of Concern •  FuncHoning of the individual and team •  FuncHoning of the research so+ware •  FuncHoning of the research field itself
  13. 13. FuncHoning of the Individual and Team •  Training & educaHon •  Ensuring appropriate credit for so+ware development •  Enabling publicaHon pathways for research so+ware •  Fostering saHsfactory and rewarding career paths for people who develop and maintain so+ware •  Increasing the parHcipaHon of underrepresented groups in so+ware engineering
  14. 14. FuncHoning of Research So+ware •  SupporHng sustainability of the so+ware •  Growing community, evolving governance, and developing relaHonships between organizaHons, both academic and industrial •  Fostering both tesHng and reproducibility •  SupporHng new models and developments (e.g., agile web frameworks, So+ware-as-a-Service) •  SupporHng contribuHons of transient contributors (e.g., students)
  15. 15. FuncHoning of the Research Field Itself •  Growing communiHes around research so+ware and disparate user requirements •  Cataloging extant and necessary so+ware •  DisseminaHng new developments •  Training researchers in the usage of so+ware •  Understanding and improving pipelines of diverse developers and maintainers
  16. 16. URSSI and Other S2I2 Projects
  17. 17. URSSI and Other S2I2 Projects Goal: Close collabora-on and fill in gaps on each axis
  18. 18. Partner with URSSI We don’t want to reinvent the wheel but partner with exisHng iniHaHves! •  UK SSI •  So+ware and data carpentries •  ACI-REF VR •  …
  19. 19. IniHal Straw Man
  20. 20. ConceptualizaHon •  Workshops •  First workshop took place in April in Berkeley •  Second workshop took place in October in Chicago •  So+ware credit workshop will take place in January in Santa Barbara •  Incubator workshop will take place in February in Maryland •  Survey with about 1200 answers – in analysis •  Ethnographic studies •  Mission and vision working group
  21. 21. How to Engage with URSSI •  Watch the website h_p://urssi.us/ •  Repos for website and workshops h_ps://github.com/si2-urssi •  Blog posts h_p://urssi.us/blog/ •  Join the mailing list h_p://urssi.us/ •  Discuss h_ps://discuss.urssi.us/ •  Twi_er h_ps://twi_er.com/si2urssi •  If you have quesHons, want to suggest something, want to volunteer, email us: contact@urssi.us
  22. 22. Technology-Enhanced Research 22 •  Increased complexity of •  today’s research quesHons •  hardware and so+ware •  skills required •  Greater need for openness and reproducibility •  Science increasingly driving policy quesHons •  Opportunity to integrate research with teaching •  Be_er workforce preparaHon We need end-to-end solu,ons that provide broad access to advanced resources and allow all to tackle today’s challenging science ques,ons è Science Gateways
  23. 23. 23 Data and compute- intensive problems High-speed networks Users generally not IT specialists Tools and workflow engines Web-based agile frameworks Distributed data and compuHng infrastructures
  24. 24. 24 Data and compute- intensive problems High-speed networks Tools and workflow engines Web-based agile frameworks Distributed data and compuHng infrastructures Users generally not IT specialists Need for science gateways!
  25. 25. 25 Data and compute- intensive problems High-speed networks Tools and workflow engines Web-based agile frameworks Distributed data and compuHng infrastructures Users generally not IT specialists
  26. 26. It’s a Science Gateway It’s a Research Portal It’s a Collaboratory It’s a Cyber- infrastructure It’s a Virtual Research Environment It’s a Virtual Lab
  27. 27. Science Gateways Gateway users are 77% of acHve XSEDE users in Q4 2016 This is largely due to the CIPRES and I-TASSER gateways, but others are gaining All users Gateways XSEDE users Login
  28. 28. Life Cycle of a Science Gateway Developers typically • work in isolaHon • must bridge to variety of resources • need building blocks in order to focus on higher-level funcHonality • struggle to secure sustainable funding Sounds familiar?
  29. 29. Science Gateway Survey 2014 30 What services would be helpful? •  sent out to 29,000 persons •  4,957 responses from across domains •  52% from life, physical or mathemaHcal sciences •  32% from computer and informaHon sciences or engineering •  45% develop data collecHons •  44% develop data analysis tools Proposed Service % Interest Evaluation, impact analysis, website analytics 72% Adapting technologies 67% Web/visual/graphic design 67% Choosing technologies 66% Usability Services 66% Visualization 65% Developing open-source software 64% Support for education 64% Community engagement mechanisms 62% Keeping your project running 62% Legal perspectives 61% Managing data 60% Computational resources 59% Mobile technology 59% Database structure, optimization, and query expertise 59% Data mining and analysis 58% Cybersecurity consultation 57% Website construction 57% Software engineering process consultation 53% Source code review and/or audit 51% High-bandwidth networks 45% Scientific instruments or data streams 44% Management aspects of a project 38%
  30. 30. Science Gateway Survey 2014 31 34% 36% 20% 17% 31% 26% 42% 16% 30% 18% 45% 44% 14% 15% 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 50% Usability Consultant Graphic Designer Community Liaison/ Evangelist Project Manager Professional Software Developer Security Expert Quality Assurance and Testing Expert Wished we had this Yes, we had this Well-designed gateways require a variety of exper-se
  31. 31. 32 “A+er all, usability really just means that making sure that something works well: that a person … can use the thing - whether it's a Web site, a fighter jet, or a revolving door - for its intended purpose without gewng hopelessly frustrated.” (Steve Krug in “Don't make me think!: A Common Sense Approach to Web Usability”, 2005) Usability
  32. 32. Technologies •  Widely used complete frameworks (Galaxy, HubZero, Globus Online etc.) •  RESTful APIs and support of mulHple programming languages in widely used frameworks (Apache Airavata, the Agave plazorm, etc.) •  Reused interface implementaHons such as the one of CIPRES with its RESTful API (CIPRES has served more than 20,000 users to date) •  Science gateways as a service with provision of hardware in the background such as SciGap (Science Gateway Plazorm as a Service) Lessons learned: approaches should be technology agnos-c, using APIs and standard web technologies OR deliver a complete solu-on Community Engagement is key Hubzero instances world wide
  33. 33. Science Gateways Community InsHtute
  34. 34. Sustainability via On-Campus Teams On-campus teams It is a centralized team at your insHtuHon – irrespecHve whether you are part of a university, a naHonal lab, an organizaHon, a consorHum or a company… Local teams vs. distributed and remote teams: For local teams it is s-ll easier to build more trust, to be more efficient and to create a strong culture. h_ps://www.codementor.io/blog/modern-engineering-teams-4ea9dp+zs Even ants wish they had an extra pair of hands when developing science gateways! • • • • • • • • • Is your campus seeing an increasing number of research projects that include web-based applications? Does each group have to hire developers independently? This can be time consuming and inefficient. You are not alone. Contact us to request a free consultation, webi- nar, or on-campus visit to start your path toward sustainable gateway development. Addressing Software Sustainability on Your Campus THEREISASOLUTION Synergy between projects http://sciencegateways.org/campusgroups help@sciencegateways.org We can provide supplemental expertise where you don’t have it. We can provide support for your journey to creating a campus-based group. We can provide ongoing advice based on campuses who have successfully created their own groups. Creating a central pool of expertise on your campus offers many benefits including: NOWISTHERIGHTTIME! INTERESTED?CONTACTUS! Science gateways are online, end-to-end solutions that provide broad access to advanced resources. They provide a community space for science and engineering research and education, allowing all to tackle today's challenging science questions. Gateways are an increasingly common component of funded activities by many agencies. Individual PIs find it challenging to recruit and sustain teams that offer the diversity of expertise necessary for developing gateways. HOWTOSTART?
  35. 35. Connect with SGCI Incubator Sustainability Bootcamp •  h_ps://sciencegateways.org/engage/bootcamp •  5 full days •  Teams on projects •  InteracHvity •  Community formaHon •  Puwng away the normal daily rouHne •  Homework •  twice per year •  addiHonal ones can be booked (travel expenses for presenters) •  adapted to feedback
  36. 36. Connect with SGCI Incubator Sustainability Bootcamp •  h_ps://sciencegateways.org/engage/bootcamp Work with us •  h_ps://sciencegateways.org/consulHng/work-with-us Yearly Conference •  h_ps://sciencegateways.org/engage/annual-conference Become involved as a partner or affiliate •  h_ps://sciencegateways.org/about/partners So+ware/Gateway Catalog •  h_ps://catalog.sciencegateways.org/ Train students in internships •  h_ps://sciencegateways.org/engage/student-focused Webinars, blogs, newsle_er, Twi_er, LinkedIn etc. h_ps://sciencegateways.org
  37. 37. Interagency Workshop 2019 Funding agencies Contact: Nancy Wilkins- Diehr wilkinsn@sdsc.edu
  38. 38. Bridging the Gap to Data Sharing Researchers “the local academic community struggles to effectively manage its assets which manifested itself in a number of challenges, and as for researchers, they lacked storage capacity and data curation processes, and the institution lacked standard metadata and indexing technologies, as well as tools that would support the whole research workflow” - Digital Asset Strategy Committee, DigitalND, 2011 Libraries Typically, data curation happens retroactively, and as a result data is either not captured at all or available metadata is incomplete. Pressures from the Outside “...digitally formatted scientific data resulting from unclassified research supported wholly or in part should be stored and publicly accessible to search, retrieve, and analyze.” - White House OSTP Public Access Memo, Feb. 2013 Image Credit Peter Alfred Hess (CC BY 2.0)
  39. 39. Current Lifecycle of Research Projects Hesburgh Libraries SelecHon/ development of tools Data assembling/ creaHng Reports PreservaHon of Data Funding ends New project Work-intensive and too late in the lifecycle
  40. 40. Target Lifecycle of Research Projects Hesburgh Libraries SelecHon/ development of tools Data assembling/ creaHng Reports PreservaHon of Data Funding ends New project EASY STEP!!! (ideally) Assure quality of data Assure quality of data
  41. 41. PresQT A collaboraHve design effort to enhance reproducibility and more open sharing of research data through open source development (July 2018-June 2020) of Tools and RESTful Services to Improve Preserva-on and Re-use of Research Data & SoXware. Hesburgh Libraries h_ps://www.imls.gov/grants/awarded/lg-72-16-0122-16 h_ps://www.imls.gov/grants/awarded/lg-70-18-0082-18
  42. 42. Hesburgh Libraries h_p://presqt.crc.nd.edu/ Two Workshops & the Needs Assessment answered by 1740 stakeholders have been completed. All Resources avail online
  43. 43. Hesburgh Libraries Collaborative Effort Where we are now
  44. 44. h_ps://osf.io/d3jx7/ h_ps://cos.io/ Project Partner An open project with all stakeholder input, workshop materials, and meeting info shared on Open Science Framework. PresQT OSF Project
  45. 45. Needs Assessment Results – over 1700 answers https://ndlib.github.io/PresQTNeeds/
  46. 46. Repository and Tool Agnostic Solutions •  Open design of tools and services using standards •  Integrate with workflows, tools, and virtual environments •  Priority Focus Areas ➔ Available for anyone to adopt what they need and build upon it!
  47. 47. Open Design Document •  Open design of tools and services using standards •  Integrate with workflows, tools, and virtual environments •  Priority Focus Areas ➔ Available for anyone to adopt what they need and build upon it!
  48. 48. Partners and Committed Collaborations •  Sheridan Libraries, John Hopkins University •  NDS •  UC San Diego Library •  HUBzero team, Purdue University •  Yale University Library •  Libraries at Amherst College, Fontbonne University, Tuskegee University, ConfederaHon of Open Access Repositories (COAR) •  ReproZip, Jupyter, CERN, RDA groups •  Midwest Big Data Hub, Science Gateways Community InsHtute, URSSI, Center for Open Science, Data CuraHon Network, So+ware PreservaHon Network
  49. 49. Partners and Committed Collaborations •  Sheridan Libraries, John Hopkins University •  NDS •  UC San Diego Library •  HUBzero team, Purdue University •  Yale University Library •  Libraries at Amherst College, Fontbonne University, Tuskegee University, ConfederaHon of Open Access Repositories (COAR) •  ReproZip, Jupyter, CERN, RDA groups •  Midwest Big Data Hub, Science Gateways Community InsHtute, URSSI, Center for Open Science, Data CuraHon Network, So+ware PreservaHon Network JOIN US!
  50. 50. Contact us: presqt-contact-list@nd.edu PresQT on the web: https://presqt.crc.nd.edu/ Subscribe to our newsletter! Hesburgh Libraries
  51. 51. Thanks! sandra.gesing@nd.edu h_p://urssi.us h_ps://presqt.crc.nd.edu h_ps://sciencegateways.org/

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