Archive for May, 2008



[CSG Spring 2008] Cyberinfrastructure Workshop – CI at UC San Diego

Cyberinfrastructure at UC San Diego

Elazar Harel

Unique assets at UCSD: CalIT2; SDSC; Scripps Institution of Oceanography

They have a sustainable funding model for the network. Allows them to invest in cyberinfrastructure without begging or borrowing from other sources.

Implemented ubiquitous Shibboleth and OpenID presence.

Formed a CI design team – joint workgroup.

New CI Network designed to provide 10 gig or multiples directly to labs. First pilot is in genomics. Rapid deployment of ad-hoc connections. Bottleneck-free 10 gig channels. Working to have reasonable security controls and be as green as possible.

Just bought two Sun Blackboxes – being installed tomorrow. Will be used by labs.

Chaitan Baru – SDSC

Some VO Projects – BIRN (www.birn.net) – NIH Biomedical Informatics Resarch Network – shares neuroscience imaging data. NEES (www.nees.org) Network for earthquake engineering simulations; GEON (www.geongrid.org) Geosciences network; TEAM (www.teamnetwork.org) field ecology data; GLEON (www.gleon.org) Global Lakes; TDAR (www.tdar.org) digital archaeology record; MOCA (moca.anthropgeny.org) comparative anthropogeny

Cyberinfrastructure at the speed of research – research moves very fast. researchers think that google is the best tool they’ve ever used – In some cases “do what it takes” to keep up: take shortcuts; leverage infrastructure from other CI projects and off-the-shelf products. Difficult because – can be stressful on developers who take pride in creating their own; engineers may think PI is changing course too many times. In other cases “don’t get too far ahead” of the users – sometimes we build too much technology – user community may see no apparent benefit to the infrastructure being developed.

The sociology of the research community influences how you think about data.

Portal-based science environments. Support for resource sharing and collaboration. Lots of commonalities, including identity and access issues. Lots of them use the same technologies (e.g. GEON and others). Ways of accessing data and instruments. Lots of interest from scientists in doing server-side processing of data rather than just sharing whole data sets for ftp. e.g. LiDAR on the GEON portal. opentopography model is an attempt to generalize that. EracthScope data portal is another example – includes SDSC, IRIS, UNAVCO (Boulder), adn ICDP (Potsdam).

Cyberdashboards – live status of information as it’s being collected. Notifications of events is also desirable.

Cyberdashboard for Emergency Response – collecting all 911 calls in California. Data miniing of spatiotemporal data. Analysis of calls during San Diego wildfires Oct 2007. Wildfire evacuations – visualization of data from Red Cross disastersafe database.

Cyberinfrastructure for Visualization

On-demand access to data – short lead times from request to readiness to rendering and display.

On-demand access to computing – online modeling, analysis and visualization tools

Online collaboration environments – software architecture, facility architecture.

SDSC/Calit2 synthesis center – conceived as a collaboration space to do science together – brings together – high performance computing; large scale data storage; in person collaboration; consultation. Has big hd screens, steroscopic screen, videoconferencing, etc. Used for workshops, classes, meetings, site visits. Needs tech staff to run it, and research staff to help with visualization, integration, data mining. So far has been on project-based funding, lately there’s been a recharge fee.

Calit2 stereo wall (C-Wall) – Dual HD resolution (1920 x 2048 pixels) with JVS HD2k projectors.

Calit2 digital cinema theater – 200 seats, 8.2 sound, Sony SRX-R110, SGI Prism with 21 TB, 10GE to computers

The StarCAVE – 30 JVC HD2k (1920 x 1080) projectors.

225 megapixel hiperspace tiled display.

In response to a question from Terry Gray, Chaitan notes that the pendulum is swinging a bit in that PIs still want to own their own clusters, but they no longer want to run them – they want them housed and administered in data centers. Elazar notes that they’re trying to make the hardware immaterial – a few years from now they may all be in the cloud, but the service component to help researchers get what they need will remain on campus.

[CSG Spring 2008] Cyberinfrastructure Workshop – Virtual Organizations

Ken Klingenstein -

An increasing artifact of the landscape of scientific research, largely from the cost nature of new instruments.

Always inter-institutional, frequently international – presents interesting security and privacy issues.

Having a “mission” in teaching and a need for administration. All of these proposals end with “in the final year of our proposal three thousand students will be able to do this simulation”. Three thousand students did hit the Teragrid a few months back for a challenge – 50% of the jobs never returned.

Tend to cluster around unique global scale facilities and instruments.

Heavily reflected in agency solicitations and peer review processes.

Being seen now in arts and humanities.

VO Characteristics – distributed across space and time; dynamic management structures; collaboratively enabled; computationally enhanced.

Building effective VOs. Workshop run by NSF in January 2008. A few very insightful talks, and many not-so-insightful talks. http://www.ci.uchicago.edu/events/VirtOrg2008/

Fell into the rathole of competing collab tools.

Virtual Org Drivers (VOSS) – solicitation just closed. Studying the sociology – org life cycles, production and innovation, etc.

NSF Datanet – to develop new methods, management structures, and technologies. “Those of us who are familiar with boiling the ocean recognize an opportunity.”

Comanage environment – externalizes id management, priveleges, and groups. Being developed by Internet2 with Stanford as lead institution. Apps being targeted: Confluence (done), Sympa, Asterisk, DimDim, Bedework, Subversion.

Two specimen VOs

LIGO-GEO-VIRGO (www.ligo.org)

Ocean Observing Initiative ( http://www.joiscience.org/ocean_observing )

The new order – stick sensors wherever you can and then correlate the hell out of them.

Lessons Learned – people collaborate externally but compete internally; time zones are hell; big turf issue of the local VO sysadmin – LIGO has 9 different wiki technologies spread out over 15 or more sites (collaboration hell). Diversity driven by autonomous sysadmins. Many instruments are black boxes – give you a shell script as your access control. Physical access control matters with these instruments. There are big science egos involved.

Jim Leous – Penn State – A VO Case Study.

Research as a process: lit search/forming the team; writing the proposal; funding; data collection; data processing; publish; archive.

Science & Engineering Indicators 2008

publications with authors from multiple institutions grew from 41% to 65%. Coauthorship with foreign authors increased by 9% between 2995 and 005.

How do we support this? Different collaborative tools. Lit Search – refworks, zotero, del.icio.us; Research info systems – Kuali Research; home grown; Proposals – wikis, google docs; etc. Lots of logins. COmanage moves the identity and access management out of individual tools and into the collaboration itself.

Need to manage attributes locally – not pollute the central directory with attributes for a specific collaboration effort.

What about institutions that don’t participate. LIGO – 600 scientists from 45 institutions.

LIGO challenges – data rates of 0.5 PB/yr across three detectors (> 1 TB /day); many institutions provide shared infrastructure, e.g. clusters, wikis, instrument control/calibration); international collaboration with other organizations; a typical researcher has dozens of accounts.

Penn State Gravity Team implemented LIGO roster based on LDAP and Kerberos – Penn State “just went out and did it” – drove soul searching from LIGO folks – “why shouldn’t we do this?”. Led to LIGO Hackathon in January, which was very productive. Implemented Shibboleth, several SPs, Confluence, Grouper, etc.

Next steps are to leverage evolving LIGO IAM infrastructure; establish permanent instance of LIFO COmanage; encourage remaining institutions to join InCommon; and (eventually) detect a gravity wave?

Bernie Gulachek – Positioning University of Minnesota’s Research Cyberinfrastructure – forming a Virtual Org at Minnesota – the Research Cyberinfrastructure Alliance.

A group of folks who have provided research technology support – academic health center; college of liberal arts; minnesota supercomputer institute; library; etc.

Not (right now) a conversation about technology, but about organization, alliances, and partnerships. Folks not necessarily accountable to each other, but are willing to come together and change the way they think about things to achieve the greater common good.

Both health center and college of liberal arts came to IT to ask how to build sustainable support for research technology .

Assessing Readiness – will this be something successful, or a one-off partnership? What precepts need to be in place for partnership? The goal is to position the institution for computationally intensive research. They have a (short) set of principles for the Alliance.

Research support has been silo’ed – need to have a connection with a specific campus organization, and the researcher needs to bridge those individual organizations. The vision is to bring the silos together. Get research infrastructure providers talking together. Researcher consultations – hired a consultant.

Common Service Portfolio – Consulting Services; Application Support Services; Infrastructure Services – across the silos. Might be offered differently in different disciplines. Consulting Services are the front door to the researcher.

Group is meeting weekly, discussing projects and interests.

[CSG Spring 2008] Cyberinfrastructure Workshop – Bamboo Project

I’m in Ann Arbor for the Spring CSG meeting. The first day is a workshop focusing on cyberinfrastructure issues.

The NSF Atkins report defines ci as high perf comp; data, information; observation, measurement; interfaces, visualization; and collaboration services. Today will concentrate on the last two.

The workshop agenda will cover interdisciplinary science; virtual organizations; visualization; mapping scientific problems to IT infrastructures; and getting CI funded.

Chad Kainz from University of Chicago is leading off, talking about the Bamboo Planning Project. The Our Cultural Commonwealth report from ACLS served the same kind of function in the humanities that the Atkins report did in the sciences.

Chad starts off with a scenario of a faculty member in a remote Wyoming institution who creates a mashup tool for correlating medieval text with maps, and publishes that tool, which gets picked up for research by someone in New Jersey, where it is used for scholarly discourse. The Wyoming faculty member then uses the fact of that discourse in her tenure review.

What if we could make it easier for faculty to take that moment of inspiration to create something and share it with others? How do we get away from the server under the desk and yet another database?

How can we advance arts and humanities research through the development of share technology services?

There are a seemingly unending number of humanities disciplines each with only a handful of people – you don’t build infrastructure for a handful of people. One of the challenges is how we boil this down to commonalities to enable working together. Day 2 of the Berkeley Bamboo workshop showed that unintentional normalization will lead to watering down the research innovations. The next workshop will start by trying to look at the common elements.

About eighty institutions participating in the first set of workshops.

One idea is to have demonstrators and pilot projects between workshops to test ideas, explore commonalities, desmonstrate shared services, and experiment with new application models. There is one project exposing textual analysis services from the ARTFL project that will probably be the first example.

New Orleans last weekend with KEXP

I realized that I hadn’t blogged about our trip to New Orleans last weekend with KEXP.The story of the discussions between KEXP and WWOZ isn’t really mine to tell (I was just there as a technology advisor), but the conversations were really interesting.

David Freedman and his ‘OZ crew were terrific hosts, and it was great to be part of an insider’s view of the Jazzfest. Everyone had interesting stories of Katrina and New Orleans pre and post. It was terribly sad to see some of the remaining devastation and drive through neighborhoods where there were still FEMA trailers in front of the houses, and to see how much abandoned and destroyed property there is.

It did seem like there was a lot of optimism in the air, and a feel of New Orleans coming back to life. Hard to say how much of that was just Jazzfest optimism.

WWOZ is an amazing part of the music community in a town where music really does matter in ways different from other places. We got to hear a lot of fabulous music – including Aaron Neville’s first appearance in New Orleans since Katrina, in the gospel tent at Jazzfest.

Some pics of the trip are here.

Pixar’s Brad Bird on innovation

The McKinsey Quarterly has an interesting interview with Pixar’s Brad Bird about innovation. I was struck by this passage, among others:

The Quarterly: If you ask most companies how they innovate, they’ll say, “Know your customer. Find out what your customer really wants you to do.” It sounds like you think about innovation differently.

Brad Bird: Our goal is different because if you say you’re making a movie for “them,” that automatically puts you on an unsteady footing. The implication is, you’re making it for a group that you are not a member of—and there is something very insincere in that. If you’re dealing with a storytelling medium, which is a mechanized means of producing and presenting a dream that you’re inviting people to share, you’d better believe your dream or else it’s going to come off as patronizing.

So my goal is to make a movie I want to see. If I do it sincerely enough and well enough—if I’m hard on myself and not completely off base, not completely different from the rest of humanity—other people will also get engaged and find the film entertaining.

Pixar’s Brad Bird on innovation

The McKinsey Quarterly has an interesting interview with Pixar’s Brad Bird about innovation. I was struck by this passage, among others:

The Quarterly: If you ask most companies how they innovate, they’ll say, “Know your customer. Find out what your customer really wants you to do.” It sounds like you think about innovation differently.

Brad Bird: Our goal is different because if you say you’re making a movie for “them,” that automatically puts you on an unsteady footing. The implication is, you’re making it for a group that you are not a member of—and there is something very insincere in that. If you’re dealing with a storytelling medium, which is a mechanized means of producing and presenting a dream that you’re inviting people to share, you’d better believe your dream or else it’s going to come off as patronizing.

So my goal is to make a movie I want to see. If I do it sincerely enough and well enough—if I’m hard on myself and not completely off base, not completely different from the rest of humanity—other people will also get engaged and find the film entertaining.

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