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Re: [stem-dev] Notes from today's STEM community call

Hi everyone,


Further to our discussions on the last conference, below is the list of modifications that some STEM help pages might need.


First of all, I would like to thank the STEM experts for their great work. While I found STEM help pages very helpful in addition to the pages as well, I have a little suggestion.


I believe everyone already knows that in software world some problems can last for unnecessarily long time to solve. As an example, when I started to learn STEM, I troubled with very slow running scenarios. After reading many pages from here and there, I started to try big solutions, such as, increasing the allocated memory to run STEM. However, when I contacted the stem-dev community, I get the answer from Jamie (many thanks to him!) by saying simply I needed to uncheck the pause feature from the preferences menu, then, I said, Ohhhhh, if I just knew this before wasting all that time.


But wait, that does not mean I am a lazy guy, on the contrary, I enjoy hardworking and learning. Nevertheless, the problem is unnecessarily wasting time, which is the scarcest resource in almost every project, don’t you think?!


Now my suggestion is, if our respectable STEM experts can spare half an hour every couple of days to set back, and run whatever screenshots capture software they have, and then start showing us how to do things. Ranging from downloading STEM, creating and running scenarios, check code, write and upload code using eGit, etc, etc, etc.


That is it! This half an hour video will for sure worth numerous pages of help documentations. Thus, I believe, if STEM experts could make a list of such videos, it will become much easier and faster for many people to get onboard and start participating effectively in using and developing STEM project.


I hope this suggestion will get your attention. Thank you.



Now, comments I have on STEM help pages are as follows:

·        The text size needs to be adjustable to suit all people, especially people who use reading glasses as I do. Windows OS has features to do this by using either the magnifier tool or changing the screen resolution, however, many disadvantages exist.

·        STEM user Help > Interface > Perspectives > Analysis

o   The new version 2.0.1 (that I am using now) has 8 taps instead of five tabs.

o   The new taps are: Error log, Time series, and Phase space.

o   Although these views and perspectives are customizable, for new users this can be confusing.

·        STEM user Help > Interface > Views > …..

o   I could not find some of the explained views when I tried to access them through:  Window > Others … > …..

o   These views are: Disease View, Report View, CSV Logger

·        STEM user Help > Interface > Wizards > New Disease

o   The list of the disease models has been changed. For example, the suggested model “Deterministic SI Disease Model Impl” does not exist in the new version software. Thus, the screen shot is different from one might see.

·        STEM user Help > Interface > Wizards > New Automatic Experiment

o   Some text seem to be cut out from the end of the page


Suggestions and comments from the community are very welcomed. Have a great weekend.

Best Regards
Hussam Ghunaim

On Thu, Aug 7, 2014 at 2:11 PM, Judy Douglas <judyvdouglas@xxxxxxxxxxx> wrote:

STEM Community Call August 7, 2014


On Call: Jamie, Stefan, Kun, Nereyda, Chris, Hussam, Judy


Introductions: Hussam Ghunaim, graduate student at the University of Bridgeport in Connecticut, plans to use STEM in doctoral dissertation



1. STEM 2.0.2 up; next release scheduled for October 22

* Chris: Date okay, not additions/issues

2. Feature request re restricting air travel for certain compartments only

* Nereyda: Will report next month when she has more specific

3. Possible use of the standards-based Systems Biology Markup Language (SBML) for predictive biological modeling

* Chris: Has successfully tried one of the tools available that supports SBML with SRI compartment model; still looking into features

* Discussion: Possible to import SBML file into STEM model builder...or vice versa?

* Chris: Export possibly easier; will attach example of what he has done this far and start discussion thread

4. Use of Levenberg-Marquardt algorithm

* Chris: Still exploring, will report

5. Comments on paper on foodborne disease published in PLoS Computational Biology

* Kun: Reader raised issue whether it is safe to assume that food is consumed where purchased

* Kun: Explained plan to explore further, including possible use of information from supermarket loyalty programs

* Jamie: Having reader comments on published paper is a rewarding experience

6. Bugs

* Stefan: All, please post any bugs on Bugzilla

* Two “bugs” currently posted are actually feature requests

* TO DO: Jamie and/or Stefan will respond to those two bugs

7. Items from participants

*Kun: Has received positive response from Journal of Food Control  on paper requesting revisions, specifically more details so readers can replicate methodology; will work on this next week and resubmit 

* Stefan: Still working on issue re checkout

* Hussam: Finding wiki documentation on STEM hard to follow; some screens outdated

** Jamie: Email pages to stem-dev

** Stefan: If trying to write a disease model, try to use model builder

** Jamie: Go to You Tube video on model builder, download automated example on Nelder-Mead



NEXT CALL: Thursday, September 4, at 9 am Pacific time


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