path: root/transcripts/fbi-diybio-2012/synbiota.mdwn

this is just a product pitch? :(

How did I get involved in the DIYbio scene? I met Derek Jacoby in summer 2010. He brought me to the biocurious space in Mountain View, in the garage. I don't have a bio-background. My background is in software. I was blown away by the stuff that the diybio community was doing, I wanted to get involved in the start. I don't have a biology background. I felt like I didn't have time to go back tos chool and learn these things to get involved.

I started to learn how this stuff works, and I learned that there is a software component. So here's an opportunity for me to make a contribution to the environment. Since then, I sort of worked with a group of people. There's two other guys that work all the time with me, and there's 6 or 7 other people that are from the open source developer community that are working on this project.

Basically what we're building is web-based open source tools for biohacker groups, professionals to do their work. Well, a big deal, there's a lot of tools where people can edit DNA. We're a little bit different. If you try to download the tools available, it's not easy to get started, there's a barrier to entry certainly for beginners.

So we have made some web-based tools where you can go to the url and you're fired up, you're starting to get work done. Instead of talk too much, I want to show you a little bit about what we have. If you notice, there's some extra information on the seats before the break that you can look at. What we have here is this sorta collaborative environment. It's almost like dropbox+github. Github is a code versioning tool. As a computer guy, I have used these tools for project and code and team management so that people can work all around the world at different times of the day.

So we tried to bring these tools to the biocommunity. So what we have here is my page, you can see here it shows some recent activity that I have been doing, these are all automatically generated. But you know, the idea is that we are focused on work. This isn't for sharing cat pictures. It's not facebook, ti's purely for work. We have a bnch of features like labbooks, projectbooks, like where you can put all that info that you are documenting, but we try to take it a step further. It's annoying and boring to type in all of your information for your labbook. I don't even use this. So the computer does things for you, if you use our design tools, when you are using actions in that tool, they will be reflected in the log book, it will alleviate some of the work. So after a long day of work, there is already stuff there, instead of writing things down for 2 hours at the end of the day.

I can quickly show you.. let's open up a project. This tool allows you to start projects and put in information about it, add colleagues, sort of like a github style way.. so I have a project here, and it's one of my kits, it's a glowing bacteria, you can see some information about it, but you can also go ahead and check out lab books, and we have ways to see people easily drag and drop iles from the lab book so that they can share it with their colleagues so thatp eople can have it all in one nice spot. So let's chekc the sequences in this project. >There are quite a bunch that are here, I can read quite a lot about them, but I cacn salso go into there and spec them and edit them. I ca bring up my editing tool which you can see here. This is a bascially text based tool where you can do editing and all that kind of stuff that you would normally do or cutting and pasting or all the normal things that people are going to do. We also have an ability to load things from external databases pretty quickly. My screen has cutoff here.

You can explore the project, here's a nice little context, you can add highlighting, here's a drop down menu. Now it appears in this window, and it's all reflected in this lab book that we have. One cool thing about this system is that since it's all javascript, it's open source for the community, so it's transparent, you guys can develop aspects that you need that we might not have, we continue to develop this.. for those who don't want to download the whole package and don't want to hack it that way, there's a straightforward plugin system, it's all javascript and jquery. I don't know if you have computer people that join your hackerspace.. most computer people know about javascript. It's a great way to get computer people involved to get them integrated and thinking the same way that you guys are.. One thing that we're working on right now is a GUI (ugh)... we can just keep adding stuff to that and it will be reflected back in that large document that I created earlier. That's basically it. The idea is to supply these tools so that people who live in a town or a city that does not have biospace physically, with a bit of learning online you can do some stuff online.. by making it open source we hope it's adopted by the open source community. We started last fall when we approached the Mozilla Foundation to see if we could get some support for this project. They agreed to give us support, not financially, but development support like security and computing back stuff that you need to know to run a sophisticated website like this, and it helps get these developers working around the globe to work on this. There are tickets on your desk with tickets.. free accounts are free to use, you cacn only make open source projects, if you want to keep your work project, it's pay, it's $7/mo to get started for private projects.. the tickets you have on your desk allows you to get a silver package for free which is $14/mo.

When are you going to add plasmid mapping? As soon as we get to it.. we havet his huge roadmap.. it all depends on how many people we get involved. We have 8 people, 3 core developers.. the guy that helped us build gentlerdesigner is one of the original developers of wikipedia.

Isn't it an igem requirement that you keep your stuff in the openwetware wiki? You can download your entire projects, xml, annotations and so on, maybe the open community will write a translator.

why would i pay for this if i can just deploy it to my own server?