Hello everyone, The first modeling bootcamp went pretty well I think, although I ended up talking the whole time so maybe others feel differently. I will strive to make this much more interactive and "workshop" like. This time, I was trying to cover as much of the tools and vision as possible. We made a video of my terminal and audio the entire time. Those videos, and the commented text from my terminal from the bootcamp are here: http://bioseed.mcs.anl.gov/~chenry/KBaseVideos/ModelingBootcamp/ I'll add the text from Sam's captionist as well, as soon as it's available. Again, please send comments and suggestions. It didn't go perfectly, and not everything is quite ready or a polished product, but this was a decent portrayal of the fulfillment of much of what I envisioned for the KBase microbes demo, so if I'm way off the mark on something, I want to know. We probably shouldn't share this first video with the community… I wasn't being careful enough with what I said to make this public. Also, there were bugs and flaws. The plan right now is to hold this bootcamp again on the following dates: 2/8: ~1-3PM 2/15: ~1-3PM 2/22: ~1-3PM The goal is to polish the tools, flag problems, identify areas for improvement, and improve the look, feel, and presentation of the workshop. This will evolve into the modeling demo we give at the GTL meeting. Sam already provided some great feedback. On the 15th or the 22nd, I think we'll produce videos and transcripts that are worthy of being shared and disseminated to the scientific community. For example, but then, we'll be running the whole thing in IRIS. I will open up the invitation for people to join the remaining bootcamps via google hangout. This time was a bit of a select crowd (microbial people who really need to see this workshop). Enjoy the videos and script (beware, it's two hours long). Hopefully we can build a tutorial from this. Best, Chris On Jan 24, 2013, at 10:33 PM, Christopher Henry <[email protected]> wrote:

Hello all,

I'm going to hold a little prototype modeling bootcamp tomorrow 1-3PM. We'll be going over the modeling tools in KBase. We'll hold it on google hangout. I'll also be recoding my screen in video, and Sam's captionist will be there (meaning we'll get a meeting transcript in writing). I'll also record the screen text of the demo. I'm hoping some of you can make it. This will be a documentation boon.

This will be the first of many such bootcamps, which I will probably hold on Fridays around the same time every week until the demo (except next week, when I'll be at Notre Dame). I expect this to evolve into our modeling demo on February 25th.

I don't expect it to go smoothly. If you want to attend one that goes really smoothly, don't come to this one… or the next one. But I do hope a core of you will come with comments that will help us to polish these services to make them "production ready". (strangely, the students in my thermo class this year didn't like it so much when I said the same thing to them)

If you can't make it because of time conflicts, then let me know. I'll adjust the specific time of the bootcamp to accommodate people.

If you plan to come, you will want to have the modeling and workspace scripts running on your machine before hand. These commands will go into IRIS, but I don't think we've got them quite yet (we are very very close… definitely by the next boot camp). So you have two options. Follow these instructions to install my little client package (not the official KBase client, although it's been working well and I think there are things we can learn from this install): https://github.com/ModelSEED/KBaseClient/blob/master/README.md

If you really don't want to bother with an install, use this server: login: kbase @128.135.250.215 pw: fbaserv!1!

Don't use that unless you are truly desperate. So the plan for tomorrow is to run through using a workspace, loading a genome, building a model, running fba, gap filling a model, loading media, loading phenotype data, simulating phenotype data, reconciling a model.

We got Pam's genomes (153 of those), the wild type shewy data, and b. subtilis data to play with. Got a lot of CDM models (100 right now). You should get a clear picture of what we've got emerging. Hopefully it's a picture that's nice for you. If it's not, hopefully you got good constructive comments on things we can do quickly to make it better.

Chris