jmuhlich

jmuhlich

Create the venv (virtual environment)

You only need to do this one time.

module avail  # look for dev/python/3
module load dev/python/3.4.2
python -m venv ~/venv   # You can replace ~/venv with any directory if you wish

Activate the venv

Do this each time you log in, before running python code.

jmuhlich

jmuhlich

import jaydebeapi
import pandas as pd

def cursor_to_df(cursor):
    df = pd.DataFrame(cursor.fetchall())
    df.columns = [d[0] for d in cursor.description]
    return df

fmsHostname = 'fmprod13.med.harvard.edu'
fmFilename = 'HITS_Reagent_Tracker_2_0'

jmuhlich

from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import (relationship, sessionmaker, subqueryload,
                            with_polymorphic)
from sqlalchemy import create_engine, Column, String, Integer
from sqlalchemy.schema import ForeignKey

Base = declarative_base()


class A(Base):

jmuhlich

import logging

logger = logging.getLogger(__name__)

def foo(a, b):
    logger.info('foo(%s, %s)', a, b)

jmuhlich

Instructions for running StarCluster on EC2 instances

Install StarCluster locally

• See documentation at http://star.mit.edu/cluster/docs/latest/installation.html
• pip install StarCluster

jmuhlich

from pysb import *

Model()

Monomer('Glucose')
Monomer('Vp')

Parameter('kf', .015)
Parameter('kr', .015)
Parameter('Vsk', -18)

jmuhlich

# Hacks to get line_profiler to profile top-level code in a script/module.

# 1. The interface only allows profiling functions, but the core profiling logic
# actually works directly with code objects. We create a new function object
# from the code at the top level of the script to profile, and call
# profile.add_function on it. This is enough to trick the bookkeeping code in
# line_profiler to include the top-level code.

# 2. Even though the entirety of the top-level code is profiled in full, the
# results printer will stop at the first function definition, class definition,

jmuhlich

import String
import Array
import Graphics.Input (Input, input)
import Graphics.Input.Field as Field

logistic : Float -> Float -> Float -> Float -> Float -> Float
logistic x emin emax mid slope =
  ( (emin-emax) / (1 + ((x/mid)^slope) ) ) + emax

lcurve : Float -> Float -> Float -> Path