[OWW-Discuss] Tapping into open source / open access and doing slightly more

Wed May 14 19:31:11 EDT 2008

BRyan,
 I don't really understand what you are proposing and if you posted an
executive summary then it might prompt more of a discussion.  I think you're
saying is that you are going to implement something and then let us see the
results, which sounds like a great way to better understand what it is you
are proposing,
cheers,
JOhn

On Wed, May 14, 2008 at 4:07 PM, Bryan Bishop <kanzure at gmail.com> wrote:

> Hey all,
>
> I am not able to attend the week-day conference calls because of high
> school scheduling issues, but otherwise I've been meaning to suggest
> something to the group. I'll just send it here instead. :-)
>
> I wrote an email about this in the context of space-based manufacturing:
> http://heybryan.org/2008-05-09.html
>
> But let me try to put things into context. I know that OWW has a good
> representation of programmers around these parts, so when I reference
> debian, I'm hoping it's not entirely lost. Take a look here:
>
> http://debian.org/ and its Wikipedia article,
> http://ubuntu.org/ And more concisely:
>  "Debian is known for strict adherence to the Unix and free software
> philosophies. Debian is also known for its abundance of options — the
> current release includes over twenty-six thousand software packages for
> eleven computer architectures. These architectures range from the
> Intel/AMD 32-bit/64-bit architectures commonly found in personal
> computers to the ARM architecture commonly found in embedded systems
> and the IBM eServer zSeries mainframes. Throughout Debian's lifetime,
> other distributions have taken it as a basis to develop their own,
> including: Ubuntu, MEPIS, Dreamlinux, Damn Small Linux, Xandros,
> Knoppix, Linspire, sidux, Kanotix, and LinEx among others. A
> university's study concluded that Debian's 283 million source code
> lines would cost 10 billion USA Dollars to develop by proprietary
> means."
>
> "Ubuntu's popularity has climbed steadily since its 2004 release. It has
> been the most viewed Linux distribution on Distrowatch.com in 2005,[4]
> 2006,[5] In an August 2007 survey of 38,500 visitors on
> DesktopLinux.com, Ubuntu was the most popular distribution with 30.3
> percent of respondents using it.[7] Third party sites have arisen to
> provide Ubuntu packages outside of the Ubuntu organization. Ubuntu was
> awarded the Reader Award for best Linux distribution at the 2005
> LinuxWorld Conference and Expo in London.[107] It has been favorably
> reviewed in online and print publications.[108][109][110] Ubuntu won
> InfoWorld's 2007 Bossie Award for Best Open Source Client OS.[111] Mark
> Shuttleworth indicates that there were at least 8 million Ubuntu users
> at the end of 2006.[112] The large user-base has resulted in a large
> stable of non-Canonical websites. These include general help sites like
> Easy Ubuntu Linux,[113] dedicated weblogs (Ubuntu Gazette),[114] and
> niche sites within the Ubuntu Linux niche itself (Ubuntu Women).[115]
> The year 2007 saw the online publication of the first magazine
> dedicated to Ubuntu, Full Circle.[116]"
>
> So, just what made these so successful? To the point where debian
> represents $10 billion USD of effort, all done by volunteer work?
> There's a bit more to mention:
>
> http://advogato.org/article/972.html
>
> "What are the issues? Why is it so important to go "distributed"?
>
> Debian is the largest independent of the longest-running of the Free
> Software Distributions in existence. There are over 1000 maintainers;
> nearly 20,000 packages. There are over 40 "Primary" Mirrors, and
> something like one hundred secondary mirrors (listed here - I'm stunned
> and shocked at the numbers!). 14 architectures are supported - 13 Linux
> ports and one GNU/Hurd port but only for i386 (aww bless iiit). A
> complete copy of the mirrors and their architectures, including source
> code, is over 160 gigabytes.
>
> At the last major upgrade of Debian/Stable, all the routers at the major
> International fibreoptic backbone sites across the world redlined for a
> week.
>
> To say that Debian is "big" is an understatement of the first order.
>
> Many mirror sites simply cannot cope with the requirements. Statistics
> on the Debian UK Mirror for July 2004 to June 2005 show 1.4 Terabytes
> of data served. As you can see from the list of mirror sites, many of
> the Secondary Mirrors and even a couple of the Primary ones have
> dropped certain architectures.
>
> security.debian.org - perhaps the most important of all the Debian
> sites - is definitely overloaded and undermirrored.
>
> This isn't all: there are mailing lists (the statistics show almost
> 30,000 people on each of the announce and security lists, alone), and
> IRC channels - and both of those are over-spammed. The load on the
> mailing list server is so high that an idea (discussed informally at
> Debconf7 and outlined here later in this article, for completeness) to
> create an opt-in spam/voting system for people to "vet" postings and
> comments, was met with genuine concern and trepidation by the mailing
> list's maintainers.
>
> It's incredible that Debian Distribution and Development hasn't fallen
> into a big steaming heap of broken pieces, with administrators, users
> and ISPs all screaming at each other and wanting to scratch each
> others' eyes out on the mailing lists and IRC channels, only to find
> that those aren't there either.
>
> So it's basically coming through loud and clear: "server-based"
> infrastructure is simply not scalable, and the situation is only going
> to get worse as time progresses. That leaves "distributed
> architecture" - aka peer-to-peer architecture - as the viable
> alternative."
>
> In other words, it's the social structure and community around debian,
> the 26,000 software packages, and that incredibly easy command where
> you can grab *any* software package and have it immediately installed.
> It's from a software repository. Kind of like biobricks, except
> functional. By that I don't mean biobricks is dysfunctional, but that
> biobricks is about data, debian's apt is about software and
> functionality.
>
> This is what one of my projects focuses on - that sort of easy gradient
> by which not only programs and software can be downloaded, but open
> access information, and open source projects of any sort, whether from
> the Maker Communities, the diybio groups, debian, gentoo, etc.
>
> For a dense explanation:
> http://heybryan.org/exp.html
>
> The 'architecture' is really ridiculously simple, it's just putting
> together some components that have been out on the web for a while. For
> example, all wikis have a revision control system, even the mediawiki
> installation for OWW. These revision systems, though, existed long
> before wikis popped up, I am particularly interested in 'git'. And for
> this reason I am also interested in ikiwiki, which can be made to look
> exactly like mediawiki, except with the important difference that it's
> based on 'git' for the revision control / history. This means that
> pages can be branched and so on, by anybody interested.
>
> It also means that you're not just providing open access data, but also
> the entire project [if the researcher is interested in going that far,
> of course]. All of the files - source code, CAD, diagrams via dia or
> graphviz, SVG, documentation, latex-source of the papers, notes, etc.
>
> It's really easy to implement.
>
> It's an extension of "open access" and "open source" in that it makes
> the whole "semantic web" thing really truly functional, making it
> actually *do* something.
>
> And it's a useful way of doing research. What's the quote? The one from
> Gregory Wilson on bottlenecks in scientific computing?
> http://www.americanscientist.org/template/AssetDetail/assetid/48548
> http://www.cs.toronto.edu/~gvwilson/<http://www.cs.toronto.edu/%7Egvwilson/>
> 'figuring out how to make scientific programmers more productive'
>
> "Those Who Will Not Learn From History..."
> Beautiful Code
> "Requirements in the Wild"
> "DrProject: A Software Project Management Portal to Meet Educational
> Needs"
> "Software Carpentry"
> Data Crunching
> "Learning By Doing: Introducing Version Control as a Way to Manage
> Student Assignments"
> "Where's the Real Bottleneck in Scientific Computing?"
> "Extensible Programming for the 21st Century"
> "Open Source, Cold Shoulder"
>
> Anyway, the only thing left for implementation is changing up mediawiki
> a bit, writing some introductory tutorials [which I am doing anyway on
> another front], and then figuring out the file structure format (using
> YAML, so it's just writing classes in python), which frankly I think is
> something that individual researchers would be more suited to doing.
> For example, that's why we have the excellent Systems Biology Markup
> Language (sbml.org), and I don't exactly have a broad enough overview
> of the field to make it happen.
>
> You get all of the benefits of software reuse, but with project reuse,
> with all of the sharing and acceleration of progress that the internet
> can allow for. So what are the general thoughts on this?
>
> - Bryan
> ________________________________________
> http://heybryan.org/
>
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-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W Providence, Rhode Island,
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