Status/purpose of biohacklabs.org?

[Ilya Levantis]

Hi all,
At some point in the past, at some DIYBio meeting or other, it was mooted that a general biohacker's wiki would be useful.
Thus, I believe, http://www.biohacklabs.org was set up.

I have some content that I would like to put up there since it is content that would benefit from edits and additions from anyone involved in DIYBio.
Is biohacklabs.org a good place to put this and are there others that would like to add content to the site?

It currently seems a bit dead - presumably because the signup is broken and you never get sent the password for an account you create.

If whoever is in charge of the site is able to fix this, should the community start putting information up there about protocols, projects etc that is useful outside each particular space's own wiki or should we just be putting things on openwetware?

I say this because lots of useful information about particular DIY protocols, equipment, etc seems to be spread across the internet with very little effort at collation. I think collation in the form of a community wide wiki (i.e. biohacklabs.org) could be a great asset, especially for those new to DIYBio.

Note: I'm not saying that everyone needs to use a centralised wiki for everything, but a page about different protocols for homemade/cheap growth media production which links to the various blog posts and instructables could be a valuable starting point for people.

Ilya

[Cathal Garvey]

Relatedly: I recently registered "biohacker.space", and some other
bright spark registered "hacker.space", so we have those safely parked
for use by global communities. If anyone has ideas for how to use
"biohacker.space" efficiently to offer subdomains and a nice central
parking zone, I'm happy to defer and set some DNS links. :)

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[Nathan McCorkle]

http://openwetware.org/wiki/Main_Page

has been stable/up for years now...

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[Cathal (Phone)]

A valuable resource but a but walled-gardeney, being awkward to join and contribute towards.

synbio.info is a shiny new (not wikimedia, I think) wiki for Synbio and already has some nice content including a map drawn from SynbioProject, IIRC. Might we worth a play around.

Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Ilya Levantis]

+1 on the walled-gardeney issue with openwetware. I also think synbio.info has a focus that doesn't necessarily fit with what would be useful for people seeking info about DIYbio topics.

[Nathan McCorkle]

On Dec 20, 2015 10:06 AM, "Ilya Levantis" <ilyale...@gmail.com> wrote:
>
> +1 on the walled-gardeney issue with openwetware.

I remember it it was just like any other site... You sign up and then wait for some real person to click 'approve'.

What is the weirdness that might be happening other than this? Deletion of content?

[Jérôme Lutz]

Hello everyone, 

I am honoured that you picked up synbio.info in your discussion, that means a lot to me - thanks! : ) 

It started out as my personal notebook in the beginning of 2015 and when I met my first SynBio friends in April this year, they asked me if I could make it public - that's how it happend and now I am spending 100% of my work time on it. My background is software dev, business and engineering - so I had to learn everything biological, and basically all I know is on there. 

In the beginning of next year, we will set up a non-profit organisation and it's mission is to bring more people into SynBio. How? 

1) First, you need to learn the (scientific) language of biology. That's why we build this Browser Extention a few days ago, it highlights words and when you click them you get the definition, see a video and can ask questions (ok, that doesnt work yet really, will take a few more days). 

2) Then you need to learn the basics of genetics, engineering concepts, etc. - that's what www.synbio.info is about 

3) Now its time to get involved, either find a job or - and I would love to work with you guys on this - find the next biohackspace and get involved there (I am often in contact with the guys from London's https://biohackspace.org, here in Berlin and Munich, we are still in the very early days).

Anyone interested in joining the mission? 

Wiki Tech

Synbio.info is based on confluence.atlassian.com, pretty much market leader in knowledge management systems. I've been working with it for 8 years and it's capabilities and user friendliness are amazing. Sure, it's not open source but I trust these guys. It's the company behind JIRA, and they have built a very special kind of company. I haven't been working a lot with Media Wiki, but from my perspective its too nerdy for the audience that we have in mind - everyone should (and is) able to edit every page, you see the edit button everywhere and no signup is required. However, people that signed up will stay updated on every page's change so that's the feedback mechanism to ensure content quality.

@Cathal: You got the domains, i got the software. When anyone wants to use them together, let us know. It took us about an hour to set up this subdomain: art.synbio.info - it has the same features as synbio.info, but its kinda standalone. We could do the same for a Biohackers wiki, if anyone is interested on working on this together.

 

@Ilya: What content are you talking about? I guess the sort of content will tell you where to put it. Also, try creating a new page on synbio.info. You will be shown a list of templates, let me know if we should add a template for protocols and stuff. 

The nice thing about using this proprietary software is that it has a huge market place: marketplace.atlassian.com. So far, we wrote 45 Apps for customizing Confluence to what we need. We will sell those apps / macros to companies that want to have the same features for their intranet (non-profits, universities, etc. will get everything for free - which is also the reason why we can use it for free). So if that works, we might even have a business model that ensures that we can persue that mission until the whole world is involved in SynBio ;-) 

OpenWet Ware

OpenWet Ware is pretty cool, but in my opinion addresses actual users & researchers in synbio, telling you what protocols do use etc. (what else can you do there?). Funny enough, just noticed that its from the BioBricks Foundation - we are currently working on another project with them.Learn "currently" now

Best, 

Jérôme

[Pieter]

I am the admin of biohacklabs.org. It was setup about 2 years ago. At the time diybio.eu was down for already a while, and we wanted to revive some of the content I once posted on that page, so registered a new domain. Also, the mailinglist of diybio.eu was a valuable list, but had no website anymore, which ment no one could find instructions on how join it anymore. So that was merged into eur...@biohacklabs.org. The mailinglist is still the most useful part of biohacklabs.org

Wikimedia is archaic technology. After being flooded by thousands of spam accounts and trying numerous dodgy plugins to fight it, I just shut down the registration. Sorry about that. There was also very little interest in posted content too. And now that it's almost 2016 I guess most people don't use wiki's anymore for sharing information. At our space it is mostly direct communication that is used, Github repo's, Slack, WhatsApp, that kind of communication. It's a pity though that those platforms are not always as open.

I've seen many attempts at centralisation of hacker/maker/fabspaces but it is kind of against the whole notion of bottom up movements to centralise. The beauty of grass roots movements is that they always use what is most useful to them, and that is different in every context. It also fits the explorative attitude of DIYBio groups to keep switching platforms and channels. That makes total sense. Those who are new will just have to find their way, asking around at your local space probably will point you in the right direction. This google group is probably the most stable factor in the community, even though it is hosted by google which should give every hacker a bad taste in his/her mouth. But it works, so that's great.

[Rajiv Patel-O'Connor]

Hey Jerome,

I'm super interested in what your doing and would love to get involved.

Best,

Rajiv Patel-O'Connor

[Jérôme Lutz]

Hey Rajiv,  that's awesome, let's do a skype call soon! You find me there under jerome.lutz.  What are you mostly interested in?  Best,  Jérôme

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[Bue Thastum]

Wikimedia is archaic technology. After being flooded by thousands of spam accounts and trying numerous dodgy plugins to fight it, I just shut down the registration. Sorry about that. There was also very little interest in posted content too. And now that it's almost 2016 I guess most people don't use wiki's anymore for sharing information. At our space it is mostly direct communication that is used, Github repo's, Slack, WhatsApp, that kind of communication. It's a pity though that those platforms are not always as open.

Wondering if wikis could get a revival if there was actually a good modern and more user-friendly alternative to Mediawiki available, which was also open source and that anyone could easily install and run on their own webpages (as with wordpress). It would be interesting to hear if anyone had any good experiences with other wiki- or wiki-like applications?

  - Bue

[Sebastian S Cocioba]

You guys should try Telegram. Open source and encrypted. File sharing on all platforms across all OSes. Seamless and gorgeous. WhatsApp can go take a hike!

Sebastian S. Cocioba

CEO & Founder

New York Botanics, LLC

Blog: ATinyGreenCell.com

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[Cathal (Phone)]

Sorry to burst that bubble, but Telegram's "Encyption" is considered laughable by anyone withzn intermediate-or-better understanding of information security. It's certainly more secure than WhatsApp by virtue of being open source (even if it's incompetent, you can be more sure it's not outright malware), and it is a non-US based service, which is nice, but that's where it ends. In all other respects, it's "considered harmful".

[John Griessen]

On 01/07/2016 09:19 AM, Cathal (Phone) wrote:
> Telegram's "Encyption" is considered laughable by anyone with . . . In all other respects, it's
> "considered harmful".

Because it lulls users into feeling safe about its possible impact on your computers/networks (attack threat)?
Could it be an easy attack avenue?

[John Griessen]

On 01/07/2016 04:26 AM, Bue Thastum wrote:
> Wondering if wikis could get a revival if there was actually a good modern and more user-friendly alternative to Mediawiki
> available, which was also open source and that anyone could easily install and run on their own webpages (as with wordpress). It
> would be interesting to hear if anyone had any good experiences with other wiki- or wiki-like applications?
>
> - Bue

Is there any FOSS wiki software that utilizes the sign ons we almost all have to google.com and facebook.com?

The anonymous defacing that wikis get is why many have given up on them just like no one operates open mail relays anymore.
Email has not died out because of the atmosphere of the internet becoming as much like a dockside city street as a TV channel.
Email FOSS, (postfix), is adding certificate based limits, no talking to unknowns, and domain name based identity checking
measures to cope. Including identity in wikis is a way forward.

[Sebastian S Cocioba]

Mind = blown. Good thing this list has some silicon savvy folks as well! 

Sebastian S. Cocioba

CEO & Founder

New York Botanics, LLC

Blog: ATinyGreenCell.com

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[Cathal Garvey]

Well, that, yes. If users think that their "private" chats are actually
private, they put themselves more at risk than if they reasonably
assumed everything was public.

Telegram uses "encryption" algorithms of their own design to promise
people security, but the algorithms are complete and utter trash, at
virtually every level. They use outdated hash algorithms, encryption
block modes that seem like they were actually not even designed for
encryption per se, and a circuitous route from text to ciphertext that
pointlessly opens up avenues of attack.

They have a "crypto contest" to break their encryption that's designed
seemingly deliberately to exclude any real-world attacks, and they admit
themselves that some forms of MITM attacks are within the reach of
consumer hardware, and ignore completely that these attacks might be
trivial for an attacker with access to special hardware (and not even
*that* special, we're talking FPGAs).

It's just...really, really rubbish. The only people saying it's even
remotely secure are Telegram themselves and hardcore users who don't
know better.

[John Griessen]

On 01/07/2016 11:11 AM, Cathal Garvey wrote:
> They use outdated hash algorithms, encryption
> block modes that seem like they were actually not even designed for
> encryption per se, and a circuitous route from text to ciphertext that
> pointlessly opens up avenues of attack.

Does it open attacks to your local network and the machine you use to access Telegram?

[Nathan McCorkle]

On Mon, Dec 21, 2015 at 3:14 AM, Pieter <pieterva...@gmail.com> wrote:
> Wikimedia is archaic technology. After being flooded by thousands of spam
> accounts and trying numerous dodgy plugins to fight it, I just shut down the
> registration.

This is a wild and ridiculous claim if you're referring to anything
but that it is written in PHP. I visit Wikipedia every day, it is
great. Does OpenWetWare get spammed? It seems not to, and I attribute
this not to plugins, but to their registration process needing human
approval.
As John Griessen asked about, yes you can use Google to sign-in, they
call it SSO (single sign on) or OAUTH2
(https://www.mediawiki.org/wiki/Extension:GoogleLogin).

> The beauty of grass roots movements is that they always use what is most
> useful to them, and that is different in every context.

That sounds more agreeable.

Your suggestion of WhatsApp is very odd to me, as I've only ever read
about WhatsApp getting hacked, leaking data, opening backdoors on
user's devices.

[Bue Thastum]

In my opinion the thing with mediawiki is that it takes too much skill, work, dedication and trial-and-error before it works acceptably. For a large project like Wikipedia that has a lot of very dedicated and technically skilled people it's not that much of a problem. For a small volunteer-run group that just wants to focus on sharing knowledge, and might not necessarily have someone with a lot experience in using a terminal for installing some extra php-library on the server that some plugin just happened to maybe need, it might end up making people give up. Also on the user end, it could be much more accessible as well, which in many situations where someone who hasn't used a wiki before just want to quickly put something up, might end up not doing it, because it appears as too much of a hassle to for instance have to understand how the the mark-up language works. (I know they've been working on making a WYSIWYG editor. Last time I tried to set it up, I couldn't make it work. It's a year and half ago, so maybe it got better in the meantime)

[Pieter]

For another project we are forking fablabs.io to create a directory of labs (not related to fabbing or bio). In case that works well, I might consider to do the same for biolabs too.
Meanwhile if anyone has more recommendations for other platforms, let me know.
I am trying to stay as true to open source and privacy friendly tools as possible, but sometimes it's just inevitable to use the dark side.
I noticed people switching to www.tiaga.io for collaborative projects and for lightweight stuff www.waffle.io (github based)

[Cathal Garvey]

I use Taiga and it's excellent. For small projects, use Kanban view, and
for larger projects, take the plunge and familiarise yourself with the
bigger, crazier mode.

The meet.jit.si module is handy too; fill the room-name box with random
letters for privacy, and encourage people to hang out there.

What Taiga is missing is a calendar module that offers ical integration,
so teams can mark tasks, events, etcetera and share timetabling. For
that, I backfill with Owncloud, hosted at owncube.com, and have them
enable the calendar addon.

I'd like to write a Webhook bridge that receives notifications from
Taiga and checks for due-dates, then uses webdav to post to
ownCloud..but webdav is such a horrid protocol and I have so little
time. :/

While we're on the subject of open groupware stuff, I'm hacking up a
personal project to enable easy self-hosted mailing lists (down with
Google!) without needing a VPS and an IP with a good reputation. I
wouldn't say it's ready for mission-critical use yet, but it does
basically work right now to host mail discussion groups:
https://github.com/cathalgarvey/listless

[Gabriela Sanchez]

Hey all,

I want to revive this discussion on developing a global platform since I also have a lot of data (and time) that I can share. Whether it be biohacklabs.org with wikimedia or some other option.

I have a suggestion!

Does anyone think that it might be useful to use Github pages? For example, Something like the [Improve this page] button on the Jekyll website which takes you directly to the Github file could kind of work like a wiki. 

The information would be publicly available in a repository. Collaborators (these would be the more dedicated volunteers) could freely contribute to the project, or any other person with a Github account; which would function as the sign on instead of google or facebook.

I am not very savvy with Github, but I think that once the layout is set up, it would be easier to contribute to. And to be honest, I would rather learn how to git, than how to wiki. Better life skill overall.

What does everyone think?

[Cathal Garvey]

I would personally advise against making oneself dependent upon
proprietary platforms of any kind if it's avoidable. Given that Jekyll /
Hugo / etc. are designed to create static HTML you can deploy literally
anywhere, *any* web-host will do.

[Gabriela Sanchez]

So, the main argument against this would be Github.

But do you think that git would be better than a wiki? I think it is useful to keep track of what changes and who is changing what.

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[Cathal Garvey]

You can use Git to version the site, and still self-host it somewhere
else. But, that doesn't even have to be Github; you could use
notabug.org or gitlab.com or even self-host using GOGS.

If you're using a VPS, You can then set up a web-server like Caddy to
pull from that repository occasionally and deploy it live:
https://caddyserver.com/docs/git

..or you could just manually upload to a shared hosting account now and
then, if you're cost sensitive. :)

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[Nathan McCorkle]

On Feb 11, 2016 8:20 AM, "Gabriela Sanchez" <sab....@gmail.com> wrote:
>
> So, the main argument against this would be Github.
> But do you think that git would be better than a wiki? I think it is useful to keep track of what changes and who is changing what.

I use github pages, I wrote a mini markup to html converter since I felt Jekyll and similars were still too heavy or involved too much setup.
http://nmz787.github.io/html/about_this_blog.html

I like that it is free, I am not depend on their closed source voodoo since I've got my local git repo... If they ever pull the free plug, I'll just upload my HTML files elsewhere, it should be easy since they're all static.

That said, since I wrote the main entries in markdown, it basically feels like a wiki with git for editing. A mediawiki install would feel a lot nicer for 'normal' scientists.

[Mac Cowell]

I have been looking into git-backed client side js wikis, I'll circle back some suggestions there later today.

Meantime, I suggest we sync the repo to multiple git servers. We could start with github bc it's so easy (and use git-hooks to automatically push it to other servers - calling Bryan Bishop... Please stand up...).

How about if Diybio.org also ran a git server? Something to look into?

Mac

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[Cathal (Phone)]

If ye have VPS then GOGS is easy to set up. And, if ye don't have HTTPS yet I recommend looking at switching to caddy to host the site, it's awesome.

[Bryan Bishop]

On Thu, Feb 11, 2016 at 11:20 AM, Mac Cowell <m...@diybio.org> wrote:

Meantime, I suggest we sync the repo to multiple git servers. We could start with github bc it's so easy (and use git-hooks to automatically push it to other servers - calling Bryan Bishop... Please stand up...).

GitHub wiki works as a git repository, push to g...@github.com:namespace/whatever.wiki.git (the .wiki.git repo is automatically setup by github). Otherwise, I suggest using ikiwiki for static html compilation from git wiki. This wiki can be hosted as a github repo as well. The github wiki git repository feature does not have all the same features as github git repos, like no pull requests or whatever. Jekyll is probably more friendly than ikiwiki, these days, even lacking the wiki front-end interface. I have found that users are profoundly confused by wikis that don't look like mediawiki's default stylesheet, so jekyll (without wiki features) seems probably fine.

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

[Gabriela Sanchez]

So it seems as if Jekyll+Github pages wins? I think that for now it might be the easiest way to start-off... Eventually we can migrate to another git repository manager—like gitlab—and another static site generator—like HUGO, and move it to our own server (eventually is the key word here).

For now, I have the resources to get it started. Anyone interested? Please share your ideas on what should the website have, look like, etc.

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Gabriela Sanchez

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[Cathal (Phone)]

If you're going with github at least do register and use a domain or subdomain you can migrate when you upgrade. Nothing worse than linkrot, and you'll lose SEO with the upgrade otherwise.

[Gabriela Sanchez]

Any suggestion for the domain? I have been calling this project “DIYbiosphere”; sphere for short. Or could we use a subdomain from the diybio.org website? 

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Gabriela Sanchez

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[Jason Bobe]

yeah, I think we could set-up a subdomain. love the name DIYbiosphere. maybe sphere.diybio.org

Jason

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[Bue Thastum]

Hi Gabriela

Cool initiative. Just from curiosity: What is the character of the data/ressources that you have and want to share?

Cheers, 

Bue

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Bue Thastum

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[Gabriela Sanchez]

As resources: I am a PhD student researching the DIYbio movement. So I have the time and funding. I am part of the Citizen Science Research team at the University of Geneva (http://citizensciences.net/). Hopefully you will be hearing from us more often! 

For the project, we are gathering a worldwide comprehensive database of all DIYbio initiatives.

We are well aware of ‘survey fatigue’ among DIYbio, therefore we are trying to construct our research in a way that is useful and meaningful for us and for the DIYbio community.

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[Bue Thastum]

That sounds really cool. I recently tried making a complete bibliography of academic litterature on DIY biology (including your thesis) as part of my current proces of writing a masters thesis in sociology about a local DIYbio community. If you're interested it's linked from here http://blog.buethastum.dk/research-on-diy-biology/

I'll start subscribing to your blog. Looking forward to see what future outputs you produce :)

[Bue Thastum]

one thing I've been thinking could be cool, would be if someone, rather than trying to map groups and labs (which is something there has already been quite a bunch of people doing or attempting, cf. for example this topic), made a really nice database of DIYbio/biohacker projects instead.