Retrieve/find data about microbial growth conditions

  • Status: Closed
  • Prize: $50
  • Entries Received: 2
  • Winner: RPaul73

Contest Brief

Dear all,

here is an explanation of the task:

In the attachment you will find a table which contains a list of microorganisms with some information about them. For a few of these microorganisms, I need to find optimal growth temperature. Here is a technical description:

• Reduce the attached table by deleting all the rows containing “sp.” symbol.
• Then reduce the table by deleting all but one species from the same genus. For instance, if the table contains several microorganisms with the same first name, such as

Escherichia coli
Escherichia albertii
Escherichia somethingelse
etc,

and each of these microorganisms has several strains, such as:
Escherichia coli O157
Escherichia coli IAI39
Escherichia coli ATCC16774
etc.

then I need to reduce the table by deleting all but one "Escherichia"-containing rows, for instance, delete all but "Escherichia coli IAI39"-containing row. By doing so for every microorganism in the table, we will get a smaller table in which every microorganism will have a unique first name.

• For the remaining species in this reduced table, please find optimal growth temperature and add these temperature values to the table
• I understand that for some species it might be tricky to find the temperature values. In this case, simply make sure that the table contains at least 100 rows for each of the following groups:
A. Psychrophiles (optimal growth below 18°C) – this first group might be smaller than 100 rows but should be bigger than 20 raws (I’m not sure if there are more than 100 microbes in nature that a capable of growth at such a low temperature)
B. Psycrhotrophes (optimal growth between 19 and 24°C)
C. Lower mesophiles (optimal growth 25-30°C)
D. Upper mesophiles (31-40°C)
E. Moderate thermophiles (growth 41-59°C)
F. Thermophiles (60-70°C)
G. Extreme thermophiles (71-80°C) – for this last group I need only more than 10 species (I’m not sure if there are enough species in nature that a capable of growing at these high temperatures)
H. Superthermophiles (above 80°C) – for this last group I don’t expect to see many species either, but more than 10 species are highly desired.

One might ask where to find the info about the optimal growth temperatures? I don't know, but in my experience there are a lot of folks here for whom this is not a problem by doing data scrapping from the world wide web. Also, please feel free to ask any questions if my explanation is not clear.

Best and many thanks for your assistance.
Sergey

PS: This is not a one-time job. I'm looking for someone to cooperate in the future to scale up this task and complete similar tasks in the coming month or two.

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Public Clarification Board

  • rinupm
    rinupm
    • 1 month ago

    I think this should have been a job rather than a contest. It is a tedious data entry with no creative aspect. Instead of one person working on a job several worked for no reason because they had no idea how many others were working on it.

    • 1 month ago
  • sergeyvmelnikov
    Contest Holder
    • 1 month ago

    For all who are going to submit the data, could you please let me know how complete is your data set? For instance: "there are 860 genuses in the reduced table and I found the optimal growth temperature for 810 of them" Otherwise it is hard for me to assess your work – I can see only a tiny piece of screenshot

    • 1 month ago
  • DaniBosch
    DaniBosch
    • 1 month ago

    Hi Sergey, I have been looking into it all day. It falls within my area of expertise so it is fun. I removed duplicated species and search in databases. However, there are no specific repositories displaying optimal temperature growth (there was one, but no longer exists). I am manually searching the literature starting with Psychrophiles, Thermophiles, and Extreme Thermophiles. This is slow work and definitely will not be completed by midnight. I can send you proof of work via chat and you should then consider the time frame. Cheers!

    • 1 month ago
    1. sergeyvmelnikov
      Contest Holder
      • 1 month ago

      Daniel, a manual search is not what I was looking for. The contest is closed.

      • 1 month ago
  • DaniBosch
    DaniBosch
    • 1 month ago

    I suggest sealing the competition to avoid copy-cuts among entries. Thanks. #sealed

    • 1 month ago
    1. sergeyvmelnikov
      Contest Holder
      • 1 month ago

      Daniel, if you complete this task by the end of the day (midnight EST) - rest assured you'll get rewarded. To avoid copy-cuts, just let me know that you are done and show a tiny piece of data, and I will trust you about the rest. Also, you can contact me via private messages. Otherwise, sealing (in my past experience) means me staying with those who talk instead of those who work.

      • 1 month ago

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