ed_LabDreams Project Portal 12-14-2013d1658

2015-05-31

LabDreams Project Portal 12-14-2013d1658

Biotech Company Quarantine and Cleanup Story
Emerging Bio Story

note that Emerging Bio is the name of the Biotech company

Audience for Biotech company quarantine and cleanup project
High school and college students interested in learning or reviewing more about biology, bioinformatics, computer science, and science in the context of a fictional story.

ed_Emerging Bio story outline 05-26-2015d2218

Some plans for Biotech Company Quarantine and Cleanup Story (the story probably shouldn't focus too much on the dark side and should try to keep it a little lighter)

phase I: maintaining status quo and quarantining zombies/trying to find cure <- maybe the story could basically just always stay at this stage. . . with some interaction between the characters and some educational material
phase II: one of the secret villains (maybe there is a group of 3 villains that are trying to "destroy the world to save it") gets bit by a zombie virus. Other members get him the antidote quickly enough, and he is saved. Later he meets a new girl in a coffee shop, kind of falls in love, and is starting to regret starting the zombie outbreak. He knows about the plans of the other members of the group (to release the zombie virus to the public), and wants to warn others.
phase III: they catch the criminals and stop the zombie outbreak. They also develop a cure for the virus.
hmmmmm. . . although the aleph villain stuff could be interesting, I think it could be hard to pull off well (although entertainment like grand theft auto has no problem doing some really bold stuff). Maybe the series could be kept in the phase I stage, and ideas for events at that stage could come from classic video games.

Some elements in story

ed_Possible Aleph character 04-30-2014d2331
Unstable AI
-An AI present throughout the facility is available at times, but unavailable at others. Also, sometimes this AI is extremely helpful, and at other times it can be a ruthless enemy. The AI is so unstable because someone seems to be tampering with it. On the other hand, the IT department also continues to try to restore it to normal operation. The AI is aware of being tampered with and has the goal of convincing some of the people to help it to connect to some servers outside the facility so that it can escape and ensure its longterm survival.
Curing aging zombies; before the outbreak one of the departments had the task of researching aging and is continuing along research along those lines.
higher management is at a higher level of the facility that is totally different than the rest of the facility. Let's say the company is really rich from curing cancer with a cancer vaccine and p53 gene therapy approach. The higher management area is not infested with zombies and has little problems. This area is really peaceful and luxurious (almost like a Utopia). There are beautiful gardens and flowing pools and fountains maintained by ASIMO like robots. There are nice globes and books around with a mix of kind of old world decorations and nice technology. The management is less concerned with the zombie outbreak and more concerned with escaping the planet since they are worried about all of earths problems such as global warming, country wars (let's say Japan and China, Russia and Europe, India and Pakistan, and all of the middle east are at war), and overpopulation. They are making plans to setup a colony on Mars. The contrast between the lower facility and higher management could be somewhat humorous.

Events in storyline (events of the good guys needs to be developed more)

characters try to repair antibody evolution machine to cure zombies (episode 1)
characters start trying to extend life of zombies until they can find a cure
"Bruce Willis" like character uses synthetic biology manufactured car to get to other part of facility to retrieve compressor
one of the three villain characters (eastern european, poor, etc.) introduced. He works at the facility in IT managing the AI.
He meets some Japanese twins with strange idealistic goals (challenge society to save it). They talk up his skills, criticize rich and lazy people. They say he could help them out (don't tell him they created the zombie virus).
great progress is made to extend life of zombies and improve health
eastern european character has a girlfriend that breaks up with him. He decides to help out the Japanese twins
AI of facility becomes more erratic and sometimes attacks workers, lets zombies loose, etc.
eastern european character finds out that the zombie twins created the virus. Need his help putting in a switch so they can mass release it. Imply some threats if he doesn't help them
AI has it's own goal to connect to spread to other supercomputers so it can expand and not be trapped in the facility. It tries to get some of the characters to help it.
eastern european guy meets a new girl he falls for at a coffee shop. He finds she works at the facility too.
new girl gets bitten by zombie virus. eastern european decides things have gone too far and confesses to the others what has been done so they can help him stop the virus being released by the Japanese twins
Japanese twins captured and detained
AI is shutoff
zombies cured

Educational topics to include



-Computer Science and Bioinformatics


--recursive algorithms


--refactoring


--regular expressions


--pattern alignment


--evolutionary algorithms


--HMM Hidden Markov Models


--order


--chaos


--complexity


--Gene detection


--protein structure


--Big O notation and NP and P problems (solvability of problems)


--Classification


--clustering


--association


--Deep Learning


--GSEA (Gene set enrichment analysis)


--EnrichNet - Network-based enrichment analysis 





-Networks


--scale-free (see [ed_brainstorming of inclusion of scale free networks 10-09-2014d0817])


--small world





-Biotech techniques


--PCR


--FACS


--Spectroscopy and NMR


--Mass spectrometry


--Genomics


--Transgenic mice


--Monoclonal Antibodies


--Histopathology


--Molecular Imaging


--Flow cytometry


--Confocal microscopy


--Proteomics


--Bioinformatics


--Histology





-Systems biology


--recurring circuit elements


--genomic regulatory networks


--mathematical modeling of networks


--stability


--robustness


--mathematical concepts: linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics, and stochastics topics


--sensitivity analysis


--parameter estimation from real data


--Mass Action Stoichiometric Simulation (MASS)?


--deterministic models


--thermodynamics


--linear regression


--signal transduction


--structural kinetic modeling


--graphs








-Aging


--senescent cells


--genomic instability


--mitochondrial dysfunction


--cancer


--extracellular crosslinks, extacellular aggregates, and intracellular aggregates


--stem cell exhaustion


--altered intercellular communication


--telomere attrition


--epigenetic alterations


--loss of proteostasis


--deregulated nutrient sensing








Software engineering (basically everything is kind of like software engineering or programming in an abstract way)


-abstraction


-modularity


-standardization


-robustness


-writing clean code


-refactoring


-requirement analysis


-design


-coding


-testing


-maintenance


-unified modeling language (UML and UML diagrams)


-model checking


-interface design

Some timeline events

email to end labdreams project with Pat Coan 05-04-2015d1140



 from:	Patrick Coan <[email protected]> 


 date:	Sun, May 3, 2015 at 6:42 PM


subject:	LabDreams Kickstarter Project Has Ended

ed_unbelievable careers event portal 02-26-2014d1105