Eric Barnhill ericbarnhill

## gist:1155906

      
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                clintel
                / gist:1155906
            
            
              Created
              August 19, 2011 02:40
            
              
                Fenced code in bullet lists with GitHub-flavoured MarkDown??
              
          
    Fenced code blocks inside ordered and unordered lists


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## pubmed_ask.r
#' Get a PubMed search index
#' @param query a PubMed search string
#' @return the XML declaration of the search
#' @example
#' # Which articles discuss the WHO FCTC?
#' pubmed_ask("FCTC OR 'Framework Convention on Tobacco Control'")
pubmed_ask <- function(query) {

  # change spaces to + and single-quotes to URL-friendly %22 in query
  query = gsub("'", "%22", gsub(" ", "+", query))

## sample.ipynb

      
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                egradman
                / sample.ipynb
            
            
              Last active
              November 2, 2022 04:59
            
              
                Simple Google Spreadsheets to Pandas DataFrame in IPython Notebook
              
          
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## search_biopython.py
# This code uses Biopython to retrieve lists of articles from pubmed
# you need to install Biopython first.

# If you use Anaconda:
# conda install biopython

# If you use pip/venv:
# pip install biopython

# Full discussion:

## keras_logistic_regression.py
from keras.models import Sequential
from keras.layers import Dense

x, y = ...
x_val, y_val = ...

# 1-dimensional MSE linear regression in Keras
model = Sequential()
model.add(Dense(1, input_dim=x.shape[1]))
model.compile(optimizer='rmsprop', loss='mse')
	#' Get a PubMed search index
	#' @param query a PubMed search string
	#' @return the XML declaration of the search
	#' @example
	#' # Which articles discuss the WHO FCTC?
	#' pubmed_ask("FCTC OR 'Framework Convention on Tobacco Control'")
	pubmed_ask <- function(query) {

	# change spaces to + and single-quotes to URL-friendly %22 in query
	query = gsub("'", "%22", gsub(" ", "+", query))
	# This code uses Biopython to retrieve lists of articles from pubmed
	# you need to install Biopython first.

	# If you use Anaconda:
	# conda install biopython

	# If you use pip/venv:
	# pip install biopython

	# Full discussion:
	from keras.models import Sequential
	from keras.layers import Dense

	x, y = ...
	x_val, y_val = ...

	# 1-dimensional MSE linear regression in Keras
	model = Sequential()
	model.add(Dense(1, input_dim=x.shape[1]))
	model.compile(optimizer='rmsprop', loss='mse')