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Literature Mining II (working with secondary data) Public

OpenWorm

Please complete the Literature Mining I badge before attempting to earn this badge, as you will be using the same tutorial materials.

Required Evidence

1) Badge Awarded for Literature Mining I

Please submit evidence (e.g. screenshot) that you have successfully earned the badge for Literature Mining I. More Info

2) Finding secondary data sources

Towlson et.al (2013) uses a secondary dataset to define the C. elegans neuronal network (the "Neuronal Networks" paper from Tutorial I). Please: a) provide a citation for this paper using the bibliographic convention of your choice, and b) please provide a link to where the data is currently stored. More Info

3) Supplemental data as secondary data

Using the file "fecundity-functions" (provided in the tutorial .zip file), please use whatever program you prefer to produce the following graph: N2 and N2(C) over time. Please label the x-axis (time in days) and the y-axis (number of offspring). * (data originally from doi.org/10.1101/045609). More Info

4) Locating data in tables and graphs

Continuing with the "fecundity-functions" data, produce a graph showing normalized peak fecundity values over time for C. elegans strains N2, aak-1,2, and daf-7. Normalize data by subtracting control conditions [c] from treatment conditions. Label each normalized series peak with maximum values. More Info

5) Locating supplemental data files

Provide a screenshot of the supplemental data file list for Li et.al (2014) from the Genome Research journal website. More Info

6) Navigating supplemental data files

For Li et.al (2014), please give a directory contents list for the data files (images and tables) that constitute the Supplemental Files. More Info

7) Locating publically-available repository data

Using Spencer et.al (2011), please: a) identify the genomic data that are publically-available, b) find an exemplar dataset using the Gene Expression Omnibus accession number, and c) provide a screenshot for this dataset (include the accession number and characteristics). More Info

Badge Experts

 

Bradly Alicea

balicea

Created badge on 9/24/16

Badge Learners