Genome Compiler

[roscoe]

I don't post much but it does seem like Genome Compiler's alpha release is out. 

 http://www.genomecompiler.com/

[Nathan McCorkle]

I really wonder if it has any useful "debugging features"

On Jun 1, 2012 4:49 PM, "roscoe" <rosco...@gmail.com> wrote:

I don't post much but it does seem like Genome Compiler's alpha release is out. 

 http://www.genomecompiler.com/

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[ruphos]

On Fri, Jun 1, 2012 at 2:28 PM, Nathan McCorkle <nmz...@gmail.com> wrote:

I really wonder if it has any useful "debugging features"

Hard to say. They don't give any info about their program (that I could find, anyway) until you click the install button. Unfortunately, they're using adobe air as a platform, which no longer supports linux-based OSes.

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-- Friedrich Nietzsche

[Bryan Bishop]

On Fri, Jun 1, 2012 at 4:34 PM, ruphos <apokr...@gmail.com> wrote:
> Hard to say. They don't give any info about their program (that I could
> find, anyway) until you click the install button. Unfortunately, they're
> using adobe air as a platform, which no longer supports linux-based OSes.

Sounds sorta useless. The only reason you might choose Adobe Air is
because you were sold over the hype about protecting your machine
code, but that's not really true because, hell, we're biohackers. The
other possible reason is some claim about cross-platform support, but
there are tons of more biologist-friendly options for that (pyjs keeps
claiming to be one, but there are others). Smells fishy to me.

- Bryan
http://heybryan.org/
1 512 203 0507

[Cathal Garvey]

...But it's not cross platform. It's Mac/Windows only.
There are oodles of other systems that are fully cross platform and more
powerful/secure than Adobe anything. Consider Python3/TclTK a nice
standard of this class.

Even properly written code in C is "cross-platform" because you can just
compile it to each architecture. Less convenient than Python, but still
miles better than Air.

Air is pretty. It might be easy to work with, I don't know. But it's not
cross-platform at all. And, as an Adobe product, it should be considered
a malware backdoor.

On 04/06/12 22:15, Omri Drory wrote:
> Hi Bryan, this Omri (CEO of Genome Compiler) - we use AIR only because of
> the cross-platform support. We're not in love with this platform and hope
> to move to HTML5 when it's mature enough.
>
> Please do try our software - there much we plan to build and support our
> community (just gave a talk at bioC + supporting iGem)
>
> Feel free to contact me at om...@genomecompiler.com if you have any feedback
>
> Omri

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[Omri Drory]

Hi Cathal, before we started coding our new version of Genome Compiler (prototype was .net/c# on win only) we looked at many tech options and had a big discussion about this. We're really tech agnostics - we only care about budding the best bioCAD tool possible and having satisfied users. 

Most likely we will need to move to another tech platform - but for now, most of our users (as based on info we get from people logging to our site) use macs/pc. We have limited personal and budget and can only do so much.

Hope you will use our web version (yes - even though it will be flash) on linux soon.

Best,

Omri

[Cathal Garvey]

I have less of an issue with web-flash, and I'll definitely give it a whirl. I do hope you can get around to implementing it as cross-platform software at some point though.

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[Meredith L. Patterson]

FWIW, the Mono implementation of the .NET runtime and C# compiler is
cross-platform. Mono is also quite a lot faster than Microsoft's .NET
implementation, though that's hard to determine because Microsoft
won't release official .NET benchmarks.

--mlp

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[Omri Drory]

Hi - we thought about mono but it didn't work for what we needed.. Again, there were no real good options. Hope HTML5/JS will get better and that the spec will be finalize so we can build the user experience we want to it (with the personal we have)

> diybio+unsubscribe@googlegroups.com.

[Cathal Garvey]

Are you familiar with the "HTML5-shiv" and other compatibility
projects/scripts? There are a bunch of these out there; they allow
legacy browsers and notoriously unreliable browsers (I'm looking at you,
IE) to render HTML5 and make certain features accessible, up to a point.

What features do you need to make HTML5/JS work well?

Nothing really makes up for the lack of standardisation, unfortunately.
If Apple would just do the internet a favour and die horribly, at least
we could get common video codecs established.

>>> diybio+un...@googlegroups.com.

>>> For more options, visit this group at
>>> http://groups.google.com/group/diybio?hl=en.
>>
>

[Omri Drory]

Hi Cathal, I'm the biologiest with the vision - not the coder with mad skilz :-)

I trust my team to let me know when the time is right to change the tech. 

Thanks for your suggestion! would also love to get some feedback on the usability of the software itself.

Omri

>>> diybio+unsubscribe@googlegroups.com.

[Connor Dickie]

For those who are interested in an accessible, cross-platform DNA design tool, Synbiota's GENtle is worth checking out at http://synbiota.com - it's an Open Source HTML5/Javascript web-based app that works right in your browser, even on a tablet. No need to install or update. It's just a web-link away like Google or Wikipedia ;-)

Like GenomeCompiler, there's a lot still to be added in terms of functionality, but it is already useful and is being used by a number of iGEM teams, DIYBio groups and University labs around the globe.

Unlike GenomeCompiler, GENtle is built on web-standards and is open source (released under the Mozilla Public License 2.0). There is an active development community at GitHub (https://github.com/Synbiota/GENtle2) where anyone can get involved to help build out features.

Just yesterday we announced the "SPrize" - a competition to incentivize the development of open source plug-ins for GENtle. Cash awards and global bragging rights are at stake!

Check it out at:

http://sprize.synbiota.com

And feel free to contact me directly at con...@synbiota.com or +1 (416) 450-9519 if you have any questions, comments or concerns. Kudos are also welcome ;-)

Regards,

Connor Dickie

Co-Founder of Synbiota

Mozilla WebFWD Fellow

[Omri Drory]

Hi Connor, I don't trash synbiota so don't trash us :-)

Just to let people know - we both came out of Singularity university (at least synbiota CEO did) - we learned from the same people there (sprize is very much taken from peter diamandis book, both have Andrew Hessel visions in mind).

I don't want to get into the religious wars between open/close free/paid software - enough to say we share the same goals of making the best tools in this field. We took different paths and we both play at our strength (like synbiota taken their weakness in fundraising and making it a strength in open source development, while we pay great people to develop). 

I say let the best program win - I do hope to work with synbiota in the future and I see we might have synergy between us. Who knows where this field us going and if a company could sustain itself at all? We believe and hope so but the road is long and uncertain. I rather have us work together then fight with each other.

As for Genome Compiler - I started this because I was pissed off no one have built a good genetic engineering software platform yet. As long as I still feel this way (I still do - even we only started and have much to go) - I will continue with my company work. I want to produce very high level product, stable, beautiful, useful and with amazing costumer support. We raised money to do so and try to be a sustainable company to we could support and build the software indefinitely. 

[Cathal Garvey]

Hi Omri,
I tried using your webapp version (I even installed Abode Flash, but
it's getting uninstalled again now that I'm finished), and it seems to
require Adobe Air even on Linux.

I'm afraid that means I'm unable to use it without installing an
outdated version of an Adobe product (they ceased supporting Air for
Linux months ago), which is personal-computing-suicide.

Thanks anyway,
Cathal

[Omri Drory]

Hi Cathal, we haven't release the web app version yet!

Let's talk on Skype (user name omri.drory) or goole hangout

[Cathal Garvey]

I would gladly, but my laptop's achilles' heel is its camera/mic combo,
and I neglected to bring my in-ear mic to work.

I look forward to trying the webapp though, if only to compare to GENtle
1/2.

[Connor Dickie]

Hey Omri,

No trashing going on. I'm sorry you felt that I was speaking negatively. I have the utmost respect for GC as we're all learning a lot from you guys. I was just stating facts In my previous message. 

Folks seem to be interested in open source, web-based HTML5 apps these days so I figured it would be useful for the community to know that Synbiota has released a Beta DNA editor that works on all operating systems via the browser - even on a tablet.

I've personally had difficulty getting GenomeCompiler working on my Linux machine and I have read that others have had similar issues. I mention Synbiota's web-based app as a potential alternative solution that people can use if they are unable or unwilling to run Adobe Air on their systems.

I also mentioned the SPrize because as a Mozillian I know that there are folks out there in the Open Source community who are interested in developing tools for Synthetic Biology. We thought that it would be great for the entire Bio Community if we could somehow unify the Open Source development efforts towards a common goal that we can all benefit from. 

Although Synbiota does not have a lot of money, we felt that it was worth scrounging up the funds to offer a series of small cash prizes as an incentive (wish we could offer millions like the XPrize). So far we have had a great response to the SPrize and even received our first code submission within the first 24 hours of the contest! We think this is pretty cool, and are excited to showcase the winning submissions in early October.

Thanks for the opportunity to clear things up Omri!

Regards,

Connor

P.S. Working together sounds like an interesting prospect! Feel free to chat with me via email/skype about this.

[Bryan Bishop]

On Mon, Jul 2, 2012 at 10:47 AM, Connor Dickie <ron...@gmail.com> wrote:

Folks seem to be interested in open source, web-based HTML5 apps these days so I figured it would be useful for the community to know that Synbiota has released a Beta DNA editor that works on all operating systems via the browser - even on a tablet

I remember checking your github repository out during the FBI workshop, and there was only a small portion of your software up as open source. :-/ Maybe Genome Compiler could release even more, like the other open source projects (say, the biolang series, etc.).

[Connor Dickie]

Hey Brian,

We do make the entire codebase for GENtle available via GitHub. GENtle is a stand-alone web-app that does not require any additional software to be useful. Anyone can download it and run it locally or host on their own web server. Some developers have already done this.

At the FBI event I demoed GENtle along with our supplementary web-based project and team management software that is free to use, but is not open source. I should have made that more clear in the demo, and has since been noted in subsequent demos that I have given.

Currently we make a hosted version of GENtle available as an open beta that anyone can use, but the supplementary tools are still in closed testing.

I hope this clears things up!

Regards,

Connor

[Omri Drory]

Ok, if you ever bring a mic (no need for camera - just want to show you stuff) just ping me.

[Omri Drory]

Like us (and almost every company on earth - google/Microsoft/github/etc) you have some open and some close source (we plan to release several open source side project like bio-file converters and other apps that we developed alongside our main effort).

We already spent ~USA$10k on supporting iGem directly and also a local iGem team. We hope to do much more with and for the community. 

We don't support Linux at the moment (flaw of the underlying tech) - hope to have a solution for those users too.

I think it's good sign to have at least 2 of our companies in this field - might have something here after all :-)

Omri

[Cathal Garvey]

Just for clarity's sake: Are you planning to release your code under an
Open-Source license once it is ready?

Omri: You may be surprised just how many successful companies there are
that share their code entirely. It's fast becoming the new norm, as
companies realise that:
A) Most customers don't *want* to roll their own: they just want to
trust the platform. Those who do roll their own, probably weren't going
to be customers anyway.
B) More often than not, the software isn't really the product, it's just
the platform. Compare this epiphany to early Rail Tycoons who didn't buy
into Air Travel because they mistakenly believed they were in the
*Rail*, and not *Travel*, business.
C) Competition is good for business. Look what happens to companies that
lack competition; they grow complacent with astonishing rapidity, and
get destroyed by new innovators. Nokia is a good example in the top-tier
domain, but it applies to companies at every level of success.
D) Code bearing a "CopyLeft" license such as the GNU license ensures
that if someone "steals" your code (if that's your attitude though, you
don't get it yet! :)), you can "steal" their improvements right back.
Open source doesn't mean "giving away": it means "sharing", or
"collaborating".

I'm not saying you guys *have* to go open source. That's your choice.
However, I think you want *us* to think that Open Source is unusual, or
impossible for you, or a bad idea. In that case, you may be barking up
the wrong tree; this community was built on the same principals as Open
Source, and it's what makes DIYbio so great and so surprisingly
successful. We don't covet our work, or our ideas, or our time; we share
it all and we receive in return.

Anyways; you don't have to accept this mindset, but don't be surprised
if some/many of us opt for the more open platform. I'll still look
forward to trying your webapp at some stage- it looks like it ticks a
lot of boxes as far as design goals are concerned, but as long as the
source remains closed/secret, I don't believe I'll adopt it for my work.

[Cathal Garvey]

I should add that the same goes for Synbiota if the source remains
closed, though GENtle2 looks really good so far (if a little unstable,
though it is beta code!). Still not as useful or versatile as GENtle,
but not far off, either.

[Omri Drory]

Hi Cathal, I get your points and don't argue them. As for what we give to the community - we give a free app for them to use (or not) + a lot of support. All of it come and will continue to come only if we will be sustainable. Being sustainable has nothing to do with close/open source - many people use and trust Google even if their core algorithms are closed and many open and closed software developers use and trust github even if github code is not a public repository on github :-). 

I want to keep high level of code and creative control on our product for now - we will release some of it as open source and we will build API for people to develop their own thing. We also don't lock users in - you can import and export your data. 

As for competition - as I said - may the best software wins. But a small/new market - small players with similar DNA (singularity university vision comes to mind) can collaborate to fight the dinosaurs in the field (cough cough vetorNTI).    

We are building our app with people like you in mind (+academics/industry) - we wish there were more people like you and more DIYbio as there's so much to do and the grand challenge of moving our civilization from finite dirty resources to renewable biological ones is huge and requires not just new tools/technology, but also many people who can harness it. 

[Cathal Garvey]

Great to hear; your attitude to development and community engagement is
great, and I look forward to seeing what code you guys do publish.

Small nitpick though:

> and many open and closed software developers use and trust github
> even if github code is not a public repository on github :-).

Github is merely a pretty shell around Git, which is entirely Open
Source. Of course I'd rather Github released all their code into the
public domain, but all that remains closed is basically their web API
wrappers around Git. The security of their site and my code, my access
to my code, and my interaction with other people's code, is entirely
conducted through Git, so I can remain assured that nothing untoward is
going on.

So yea, Github is a contradiction; Open-Source advocates, with an Open
Source platform, but with a Closed-Souce webapp. It's a pain. :)

[Dakota Hamill]

I installed and played around with Gnome Compiler for a while.  I liked the look of the software, very colorful and interactive, reminded me of Spore for some reason.  I think the idea of drag, drop, n shop for DNA pieces is awesome.  It saddens me to see all those great BioBrick pieces in there, but know I'll never be able to (for now) ever order them. 

I am most looking forward to being able to use the Metabolic pathway search, it looked great in the demo video.

A few small suggestions:

 It'd be great to have a circular overview of a plasmid, just because I think many people are used to seeing them like that, myself included.  Manipulating the genes on the horizontal layout is perfect, but on the "genome" zoomout view it'd be sweet to see them as a circle with all the restriction cut sites and labelled genes.  

It'd also be nice to have a small popout info window when browsing through the materials and pieces, without having to drag and drop the pieces into the main screen.  There are tons of iGem biobrick parts, and I like just surfing through them at random and seeing what is out there, ya never know what you may stumble upon that could inspire some new piece of DNA.  That being said, I'm not going to drag and drop every single one to the center of the screen, and close each window.  Having a brief overview window that updates in real-time with basic info would be fantastic.

Also, I don't know how difficult it would be, but being able to explore all of the BioBricks "in house" would be  good too, without the need for the registry website.  I was wanting to find some Lux genes, but Lux yields no search returns, even though in the description of some of the biobrick parts the words Lux do appear often (does the search only target specific fields, and ignore others?).  So I had to go to the registry website, find some Lux Bba_ ID's then come back and search them out in Genome Compiler.  Not a huge inconvenience by any means but, it'd be nice to stay inside the software.      

Searching "Amp" only yields an E.Coli strain and a bacteriophage, maybe that was by design, but it'd be nice to see all things that have the Amp gene in them.  I know some plasmids have them, and I think it'd be a great way to be exposed to new plasmids you might not normally chose, but that have some of the desired features you want (like Amp resistance).  Something along the lines of, "hey pUC18 is my go-to screening plasmid, but I'd really like another plasmid with more cut sites in the Amp gene, let me search for Amp and find a new plasmid - maybe pBR322 will work.

So in that sense, I think the search function could use a little boost.

Besides that I could see myself using the software in the future, though I havn't used the "check price" now function.  Keep up the interesting work.

-Dakota

[Omri Drory]

Hi Dakota, thanks for the feedbacks!

All your suggestions are great, and many of them were submitted to us - on our roadmap we have some big updates soon(TM) - Sequence detection for restriction enzymes (our graphic designer is doing amazing job there - going to look and feel much better then anything else in the field), multiline of genetic data (now only show one horizontal line - will show more lines of data as you increase the size of the window) and direct connection to the NCBI database from the search box (so you don't have to go to NCBI and use it's notoriously bad search to find genetic parts and genomes). After that release we have several features that includes better search in the material box coming. Stay tuned!

Please feel free to add more feature requests/bugs/enhancements at genomecompiler.com/feedback

Omri

[Omri Drory]

Hi Guys, An interview I gave with the tech zing guys (Who also did a great interview with Catahl a few weeks ago) is live now. It has some additional information about Genome Compiler past and plans. Check it out here: http://techzinglive.com/page/1124/196-tz-discussion-omri-drory-genome-compiler