Hashtag= #SpaceMicrobes / $SciStarter
Project website : http://spacemicrobes.org
Space station Microbiome
What kinds of microbes live on the surfaces inside the International Space Station (ISS)? We’ll be asking astronauts to swab the Space Station and send these samples back to Earth. Using DNA sequencing, we will be able to investigate and analyze patterns in microbial communities.
Swabbing Stadiums & Space Meetups
How do microbes differ across different types of surfaces in a building? And how do Earth surfaces compare to those in space? Here on this planet, we’ll be collecting swab samples at sporting events, space meetups, and other public events across the USA. We’ll be sampling microbes that live on cell phones, shoes and surfaces (keyboards, screens, railings, etc).
Microbial Playoffs... in SPAAAAAAACE!
How will microbes from YOUR favorite arena perform in the space playoffs? At UC Davis, we’ll be growing microbes from samples collected at sporting events across the country. Microbes that impress us during their training camp in our laboratory will be sent to the Space Station for a zero-gravity growth competition. We’ll track what bacteria grow the fastest in space and compare these stats to the microbial competitors on Earth.
We have three areas where software can help:
- Sample collection : We have over two thousand individual samples to track, along with metadata and informed consent documentation for each.
- Progress tracking : One of the most important aspects of research is keeping all of the researchers up-to-date on the status of each part of the project. Normally, there are only a handful of scientists involved in a project, and so they can sit down and have meetings. However, this is a citizen science project. There are thousands of researchers!
- Visualization and analysis : Microbes form entire ecosystems that are difficult to understand intuitively; a quantitative approach is essential. Normally, this takes the form of a data matrix visualized as a "heatmap." Ecological relationships are explored using clustering algorithms.
- We have developed a prototype web application for registering sample, collecting metadata and creating a database of all of this information, but a mobile app would be even better.
- A tool for keeping citizen scientist up-to-date about the status of the research as it proceeds, especially aboard the Space Station.
- A mobile app for creating, sharing and manipulating heatmaps of ecological data.
Sample Registration Webapp : https://github.com/ryneches/samplereg
Specifications & Requirements: Registering Samples
- Users must be presented with a clear, simple statement about privacy and liability, and our rules. If they are minors, we need to think about the correct way to handle this, since they cannot legally agree to anything.
- The app should collect the following pieces of data :
- The sample tracking number from a barcode or QR code
- A photograph of the sample surface
- A photograph of the "big picture" context
- The phone's current GPS/network location
- The type of surface (metal,stone,plastic,glass,wood...)
- The surface temperature (strip thermometer)
- The surface humidity (dry, damp, wet)
- A general description (about 140 characters)
- General description of the event ("Redskins game")/location and date of sampling
- The sampling kits will each be labeled with both a human readable unique identifier and a barcode QRcode. If possible, we would very much like for the sample registration component to be able to read the barcode, and to use the device's internal GPS to populate the latitude and longitude fields.
- The sample registration table has a field for the auditing status of the sample. This field will be used to indicate the current status of the sample as it moves along our process. This would make it possible to provide users notifications as their sample is received by our lab, as it is checked for damage, as its registration data is vetted, when we proceed with DNA extraction, when it is prepared for DNA sequencing, when it is actually running on the sequencing machine (this can take several days), when the sequencing is completed, when we do our initial checks to verify that the sample was sequenced correctly, and when it moves into our statistical analysis.
- The sample record table will have geolocation fields and a number of (hopefully) useful fields describing the surface from which it was taken. Along with the auditing status, this could be used in variety of interesting interfaces for tracking the status of an individual sample, a team's samples, or the project overall.
- The app should save the submission locally, in case the upload breaks for some reason. Also, people might not have a data plan, or a very good data plan. It should also give confirmation of a successful upload, and confirmation once the submission has been reviewed and put into the database. The confirmation could be via SMS and/or email.
- The app should allow the user to review their own submissions in list form and on a map.
Communicating project status, displaying data
- This is where we have a huge amount of flexibility. It could be making the raw data available as we receive it. It could be posting updates to the project website (there is going to have to be one, even if it's a "headless" API for the app to upload data into). It could be emailing users individualized reports about their samples. It could be mailing them physical printouts of their data, or three dimensional representations manufactured on 3D printers, or cool posters or plaques.
- We'd like to integrate the findings (visualize the analysis via color coded dots, for example) with existing NASA tools that track the path of the ISS and allow people to sign up for alerts when the ISS is going to pass overhead.
- We would like to have let the participants help analyze the raw data. We could hold a couple of contests, and give out prizes. For example, "Best Science Fair Entry," "Best Graphic," "Best Diagram," "Best Overall Analysis," and "Best Essay." We'll have a message board where people can post questions as they work, and the microbiologist on our team will do our best to answer them. The best of that material will go into the paper (all participants will be credited in the paper, regardless).
Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization
Sample code for a user registration systemhttps://github.com/ryneches/samplereg
Project MERCCURI: Space Station Microbiome and Microbes in Spacehttp://www.microbe.net/project-iss-microbiome-collaboration-with-science-cheerleaders/
A nice, simple description of the research project as well as an archive of developments and events.
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