Jupyter Notebooks in EuropePMC
 Share
The version of the browser you are using is no longer supported. Please upgrade to a supported browser.Dismiss

 
£
%
123
 
 
 
 
 
 
 
 
 
 
 
 
 
 
FHADAEAFAGAH
1
PMC URLtitleNotebook URLCode in problem cellProblemCommentsLicense
2
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296728Diversity and composition of the adult fecal microbiome associated with history of cesarean birth or appendectomy: Analysis of the American Gut Project.http://nbviewer.jupyter.org/github/biocore/American-Gut/blob/master/ipynb/module2_v1.0.ipynb%run cluster_utils.ipy
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-2-047f4397506b> in <module>()
7 from tempfile import mktemp
8 from collections import defaultdict
----> 9 from cPickle import loads
10 from itertools import izip
11 from ftplib import FTP

ModuleNotFoundError: No module named 'cPickle'
3
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976103Software Carpentry: lessons learned.n/a
4
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448745ActivePapers: a platform for publishing and archiving computer-aided research.n/a
5
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278760An antidote to the imager's fallacy, or how to identify brain areas that are in limbo.http://nbviewer.jupyter.org/github/Gilles86/in_limbo/blob/master/notebooks/level2_simple.ipynb
import nipype.algorithms.modelgen as model
import pandas
import nipype.pipeline.engine as pe
from nipype.interfaces.base import Bunch

import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-1-4549179c63f3> in <module>()
----> 1 import nipype.algorithms.modelgen as model
2 import pandas
3 import nipype.pipeline.engine as pe
4 from nipype.interfaces.base import Bunch
5

ModuleNotFoundError: No module named 'nipype'
6
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267933Fast and efficient Drosophila melanogaster gene knock-ins using MiMIC transposons.n/a
7
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150318Stress-induced mutagenesis and complex adaptation.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150318/bin/rspb20141025supp2.txtprint "VERSIONS" File "<ipython-input-1-981a4c563a59>", line 1
print "VERSIONS"
^
SyntaxError: Missing parentheses in call to 'print'
8
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4092319Enriched biodiversity data as a resource and service.http://nbviewer.ipython.org/urls/raw.githubusercontent.com/myGrid/DataHackLeiden/alan/Player_example.ipynb?create=1
9
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906378Powerlaw: a Python package for analysis of heavy-tailed distributions.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906378/bin/pone.0085777.s003.ipynb
10
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270252Perceived displacement explains wolfpack effect.https://github.com/simkovic/wolfpackRevisited/blob/master/code/Revision1.ipynbseveral in https://github.com/simkovic/wolfpackRevisited/tree/master/code
11
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670004CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.http://nbviewer.jupyter.org/github/idekerlab/py2cytoscape/blob/develop/examples/New_wrapper_api_sample.ipynb
from py2cytoscape.data.cynetwork import CyNetwork
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import StyleUtil
import py2cytoscape.util.cytoscapejs as cyjs
import py2cytoscape.cytoscapejs as renderer

import networkx as nx
import pandas as pd
import json
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-4-e71522d3c65d> in <module>()
----> 1 from py2cytoscape.data.cynetwork import CyNetwork
2 from py2cytoscape.data.cyrest_client import CyRestClient
3 from py2cytoscape.data.style import StyleUtil
4 import py2cytoscape.util.cytoscapejs as cyjs
5 import py2cytoscape.cytoscapejs as renderer

ModuleNotFoundError: No module named ''py2cytoscape"
12
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559436ReproPhylo: An Environment for Reproducible Phylogenomics.http://nbviewer.jupyter.org/github/HullUni-bioinformatics/ReproPhylo/blob/master/Tutorial_files/Git/Git_Demo.ipynb
13
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588804Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases.n/a
14
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355505Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients.http://nbviewer.jupyter.org/github/biocore/American-Gut/blob/master/ipynb/Alpha%20diversity%20notebook.ipynb
from americangut.diversity_analysis import (check_dir, pad_index, pretty_pandas_boxplot)
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-1-cc86e0879fa9> in <module>()
6 from pandas import read_csv, Series, DataFrame
7 from IPython.display import Image
----> 8 from americangut.diversity_analysis import (check_dir,
9 pad_index,
10 pretty_pandas_boxplot)

ModuleNotFoundError: No module named 'americangut'
15
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355505Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients.http://nbviewer.jupyter.org/github/biocore/American-Gut/blob/master/ipynb/Power.ipynbcss_file = './ag.css'---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-1-2d0bde900447> in <module>()
3 from IPython.core.display import HTML
4 css_file = './ag.css'
----> 5 HTML(open(css_file, "r").read())

FileNotFoundError: [Errno 2] No such file or directory: './ag.css'
16
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412813Orthogonalization of regressors in FMRI models.http://nbviewer.jupyter.org/github/jmumford/orthogonalizaton_ipynb/blob/master/orthogonalization.ipynb
17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755742Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration.http://nbviewer.jupyter.org/gist/fabianrost84/3cc58a27b5688f4e2eba
import scipy as sp
import pandas as pd
import matplotlib.pyplot as plt
%matplotlib inline
import probfit
import iminuit
import warnings
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-1-3648e5abbe81> in <module>()
3 import matplotlib.pyplot as plt
4 get_ipython().magic('matplotlib inline')
----> 5 import probfit
6 import iminuit
7 import warnings

ModuleNotFoundError: No module named 'probfit'
18
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496567Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial).http://nbviewer.ipython.org/github/germs-lab/frontiers-review-2015/blob/master/frontiers-nb-2015.ipynb!bash install-megahit.shbash: install-megahit.sh: No such file or directory
19
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658184Computing Workflows for Biologists: A Roadmap.n/a
20
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631998Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations.http://nbviewer.jupyter.org/github/JonM4024/synthetic_lethals/blob/master/double_deletions_example.ipynbfrom cobra.flux_analysis.double_deletion import double_gene_deletion_fba, double_reaction_deletion_fba
from cobra.io import load_matlab_model, save_matlab_model
import pandas as pd
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-aab1d47f733e> in <module>()
----> 1 from cobra.flux_analysis.double_deletion import double_gene_deletion_fba, double_reaction_deletion_fba
2 from cobra.io import load_matlab_model, save_matlab_model
3 import pandas as pd

ImportError: No module named 'cobra'
cobrapy is listed as a dependency
21
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881760Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing.http://nbviewer.jupyter.org/github/a-slide/iPython-Notebook/blob/master/Notebooks/VCF_analysis.ipynbmultiple notebooks in repo
22
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379514Improving functional magnetic resonance imaging reproducibility.n/a
23
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517073Lessons from Fraxinus, a crowd-sourced citizen science game in genomics.http://nbviewer.jupyter.org/github/shyamrallapalli/fraxinus_version1_data_analysis/blob/master/fraxinus_visits_model/Players-nonplayers.ipynb
24
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491703The number of olfactory stimuli that humans can discriminate is still unknown.n/a
25
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528367Data analysis as a source of variability of the HLA-peptide multimer assay: from manual gating to automated recognition of cell clusters.https://duke.app.box.com/s/9kphs2300kumjyowjq06
# Python modules
import fcm
import fcm.statistics as stats
import os, sys, glob
import numpy as np
from pandas import DataFrame, Series
import pandas as pd
ImportError Traceback (most recent call last)
<ipython-input-2-5e0336f85338> in <module>()
1 # Python modules
----> 2 import fcm
3 import fcm.statistics as stats
4 import os, sys, glob
5 import numpy as np

ImportError: No module named 'fcm'
26
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669674Tracing regulatory routes in metabolism using generalised supply-demand analysis.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669674/bin/12918_2015_236_MOESM5_ESM.ipynb
%matplotlib inline
import pysces #Python Simulator for Cellular Systems
import psctb #PySCeSToolbox
import numpy
ImportError Traceback (most recent call last)
<ipython-input-1-f62aadde36c9> in <module>()
1 get_ipython().magic('matplotlib inline')
----> 2 import pysces #Python Simulator for Cellular Systems
3 import psctb #PySCeSToolbox
4 import numpy

ImportError: No module named 'pysces'
27
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972086An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.http://nbviewer.jupyter.org/github/maayanlab/Zika-RNAseq-Pipeline/blob/master/Zika.ipynb
28
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034285A 2D virtual reality system for visual goal-driven navigation in zebrafish larvae.https://github.com/ajouary/VR_Zebrafish/blob/master/Code/FishTracking.ipynb%run FunctionImageTracking.py
%matplotlib inline
ImportError Traceback (most recent call last)
/home/paws/PMC-Jupyter-reruns/FunctionImageTracking.py in <module>()
10 import matplotlib.pyplot as plt
11
---> 12 import skimage
13 import skimage.filters as skif
14 import skimage.data as skid

ImportError: No module named 'skimage'
29
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049846Integrity of the Human Faecal Microbiota following Long-Term Sample Storage.http://nbviewer.jupyter.org/github/biocore/American-Gut/blob/master/ipynb/module2_v1.0.ipynb
30
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940747Tools and techniques for computational reproducibility.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940747/bin/13742_2016_135_MOESM3_ESM.ipynb"I couldn't find a kernel matching Python 2. Please select a kernel:"
31
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014984Datathons and Software to Promote Reproducible Research.Notebook shared as a figure only! https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014984/figure/figure1/
32
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4946111Where next for the reproducibility agenda in computational biology?
33
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199146The importance of digitized biocollections as a source of trait data and a new VertNet resource.
34
NAWhat's What: The (Nearly) Definitive Guide to Reaction Role Assignment.
35
NANeurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.
36
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5145134Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.
37
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123367Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.
38
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870738Recommendations for open data science.
39
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119319jicbioimage: a tool for automated and reproducible bioimage analysis.
40
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787049Systems biology of the structural proteome.
41
NAAccelerate Healthcare Data Analytics: An Agile Practice to Perform Collaborative and Reproducible Analyses.
42
NAYeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation.
43
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118469Pyrcca: Regularized Kernel Canonical Correlation Analysis in Python and Its Applications to Neuroimaging.
44
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050205(13)C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids.
45
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319736Kepler WebView: A Lightweight, Portable Framework for Constructing Real-time Web Interfaces of Scientific Workflows.
46
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795700Activation of G Proteins by Guanine Nucleotide Exchange Factors Relies on GTPase Activity.
47
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868476Reticulate evolution is favored in influenza niche switching.
48
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5101613A public data set of human balance evaluations.
49
NAAn accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses.
50
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053501Language-Agnostic Reproducible Data Analysis Using Literate Programming.
51
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054807The 2016 Bioinformatics Open Source Conference (BOSC).
52
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936733A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research.
53
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5173344Beyond Academia - Interrogating Research Impact in the Research Excellence Framework.
54
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720982REPRODUCIBLE AND SHAREABLE QUANTIFICATIONS OF PATHOGENICITY.
55
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4963212Accurate Reconstruction of Cell and Particle Tracks from 3D Live Imaging Data.
56
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834562PyRhO: A Multiscale Optogenetics Simulation Platform.
57
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858870High-performance web services for querying gene and variant annotation.https://github.com/sulab/myvariant.info/blob/master/docs/ipynb/myvariant_R_miller.ipynb
58
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4975741A preliminary review of influential works in data-driven discovery.n/a
59
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018365MEANS: python package for Moment Expansion Approximation, iNference and Simulation.n/a
60
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928468A General Procedure to Study Subcellular Models of Transsynaptic Signaling at Inhibitory Synapses.https://collab.humanbrainproject.eu/#/collab/704/
61
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069772Avoiding Pandemic Fears in the Subway and Conquering the Platypus.http://goo.gl/UIhBjf
62
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5162102A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence.https://github.com/scanisius/discover-notebooks
63
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911401From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model.https://github.com/linsalrob/PyFBA/blob/working/iPythonNotebooks/From_functional_roles_to_gap-filling.ipynb; https://github.com/linsalrob/PyFBA/blob/working/iPythonNotebooks/Using_an_SBML_model.ipynb
64
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008457Real-time selective sequencing using nanopore technology.https://github.com/mattloose/RUFigs
65
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5182066Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls.https://doi.org/10.5281/zenodo.160333
66
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021153From big data to deep insight in developmental science.n/a
67
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988647FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.n/a
68
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965465Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.http://nbviewer.ipython.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb
69
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917969Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer.https://github.com/PeterUlz/FocalAmplifications/tree/master/Focal_amplifications_in_R.ipynb
70
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5140024COMPASS: Continuous Open Mouse Phenotyping of Activity and Sleep Status.https://github.com/LozRiviera/COMPASS_paper
71
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739432Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project.http://nbviewer.ipython.org/github/biocore/American-Gut/blob/master/ipynb/module2_v1.0.ipynb
72
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019306Using Machine Learning and Natural Language Processing Algorithms to Automate the Evaluation of Clinical Decision Support in Electronic Medical Record Systems.n/a
73
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167163Evaluating the evaluation of cancer driver genes.https://github.com/KarchinLab/Tokheim_PNAS_2016
74
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817224Real-time, portable genome sequencing for Ebola surveillance.http://github.com/nickloman/ebov
75
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5095137Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience.http://tinyurl.com/zq6uuja
76
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055122Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.http://github.com/linnarsson-lab/ipynb-lamanno2016
77
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069741Geography and Location Are the Primary Drivers of Office Microbiome Composition.https://github.com/gregcaporaso/office-microbes
78
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878278MIMIC-III, a freely accessible critical care database.https://github.com/MIT-LCP/mimic-iii-paper/blob/master/notebooks/tsne-vis.ipynb
# imports import numpy as np import pandas as pd import matplotlib.pyplot as plt %matplotlib inline import psycopg2 from sklearn.manifold import TSNE from sklearn.preprocessing import MinMaxScaler
ValueError Traceback (most recent call last)
<ipython-input-2-218ac2cc07df> in <module>()
1 # imports
2 import numpy as np
----> 3 import pandas as pd
4 import matplotlib.pyplot as plt
5 get_ipython().magic('matplotlib inline')

//anaconda/lib/python3.5/site-packages/pandas/__init__.py in <module>()
42 import pandas.core.config_init
43
---> 44 from pandas.core.api import *
45 from pandas.sparse.api import *
46 from pandas.stats.api import *

//anaconda/lib/python3.5/site-packages/pandas/core/api.py in <module>()
7 from pandas.core.common import isnull, notnull
8 from pandas.core.categorical import Categorical
----> 9 from pandas.core.groupby import Grouper
10 from pandas.core.format import set_eng_float_format
11 from pandas.core.index import Index, CategoricalIndex, Int64Index, Float64Index, MultiIndex

//anaconda/lib/python3.5/site-packages/pandas/core/groupby.py in <module>()
15 from pandas.core.base import PandasObject
16 from pandas.core.categorical import Categorical
---> 17 from pandas.core.frame import DataFrame
18 from pandas.core.generic import NDFrame
19 from pandas.core.index import Index, MultiIndex, CategoricalIndex, _ensure_index

//anaconda/lib/python3.5/site-packages/pandas/core/frame.py in <module>()
39 create_block_manager_from_arrays,
40 create_block_manager_from_blocks)
---> 41 from pandas.core.series import Series
42 from pandas.core.categorical import Categorical
43 import pandas.computation.expressions as expressions

//anaconda/lib/python3.5/site-packages/pandas/core/series.py in <module>()
2907 # Add plotting methods to Series
2908
-> 2909 import pandas.tools.plotting as _gfx
2910
2911 Series.plot = base.AccessorProperty(_gfx.SeriesPlotMethods, _gfx.SeriesPlotMethods)

//anaconda/lib/python3.5/site-packages/pandas/tools/plotting.py in <module>()
26 from pandas.util.decorators import Appender
27 try: # mpl optional
---> 28 import pandas.tseries.converter as conv
29 conv.register() # needs to override so set_xlim works with str/number
30 except ImportError:

//anaconda/lib/python3.5/site-packages/pandas/tseries/converter.py in <module>()
5 from dateutil.relativedelta import relativedelta
6
----> 7 import matplotlib.units as units
8 import matplotlib.dates as dates
9

//anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in <module>()
1129
1130 # this is the instance used by the matplotlib classes
-> 1131 rcParams = rc_params()
1132
1133 if rcParams['examples.directory']:

//anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in rc_params(fail_on_error)
973 return ret
974
--> 975 return rc_params_from_file(fname, fail_on_error)
976
977

//anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in rc_params_from_file(fname, fail_on_error, use_default_template)
1098 parameters specified in the file. (Useful for updating dicts.)
1099 """
-> 1100 config_from_file = _rc_params_in_file(fname, fail_on_error)
1101
1102 if not use_default_template:

//anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in _rc_params_in_file(fname, fail_on_error)
1016 cnt = 0
1017 rc_temp = {}
-> 1018 with _open_file_or_url(fname) as fd:
1019 try:
1020 for line in fd:

//anaconda/lib/python3.5/contextlib.py in __enter__(self)
57 def __enter__(self):
58 try:
---> 59 return next(self.gen)
60 except StopIteration:
61 raise RuntimeError("generator didn't yield") from None

//anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in _open_file_or_url(fname)
998 else:
999 fname = os.path.expanduser(fname)
-> 1000 encoding = locale.getdefaultlocale()[1]
1001 if encoding is None:
1002 encoding = "utf-8"

//anaconda/lib/python3.5/locale.py in getdefaultlocale(envvars)
556 else:
557 localename = 'C'
--> 558 return _parse_localename(localename)
559
560

//anaconda/lib/python3.5/locale.py in _parse_localename(localename)
484 elif code == 'C':
485 return None, None
--> 486 raise ValueError('unknown locale: %s' % localename)
487
488 def _build_localename(localetuple):

ValueError: unknown locale: UTF-8
Several notebooks in https://github.com/MIT-LCP/mimic-iii-paper/ .

All gave
"I couldn't find a kernel matching Python 2. Please select a kernel:"

and then came up with error messages like the ones listed in the left column.
79
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072699Ten Simple Rules for Digital Data Storage.n/a
80
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC-7006The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Disseminationn/a
81
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779235Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets.https://github.com/isidroc/bioalerts
82
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980007Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes).https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980007/bin/pone.0159762.s001.html
83
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014103Geophysical fluid dynamics: whence, whither and why?n/a
84
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999233Evidence of Online Performance Deterioration in User Sessions on Reddit.
85
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4805879Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.n/a
86
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890304Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish.http://github.com/chewgl/uORF_repressiveness_supplemental/
87
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884666Computational virology: From the inside out.https://github.com/scipy/scipy/pull/5232
88
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986259A comprehensive and scalable database search system for metaproteomics.n/a
89
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791574Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery?https://github.com/ipython/docker-notebook
90
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051545Finding Our Way in the Dark Proteome.n/a
91
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189966Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189966/bin/ppat.1006114.s013.zip
92
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841782Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.https://dx.doi.org/10.7554/eLife.12741.029; https://dx.doi.org/10.7554/eLife.12741.030
93
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069746From Sample to Multi-Omics Conclusions in under 48 Hours.
https://github.com/biocore/american-gut/blob/master/ipynb/primary-processing/02-filter_sequences_for_blooms.md
94
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5158082Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus.n/a
95
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148610Connectivity map of bipolar cells and photoreceptors in the mouse retina.https://github.com/berenslab/pr_bc_connectivity
96
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941947Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons.https://github.com/Schork-Lab/np_single_nucleus_rnaseq/
97
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073428BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.n/a
98
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979073Markov chain evaluation of acute postoperative pain transition states.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979073/bin/NIHMS798127-supplement-Supplementary_Materials__Appendix_1.html
99
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885855Modeling Interactions between Speech Production and Perception: Speech Error Detection at Semantic and Phonological Levels and the Inner Speech Loop.Downloadable at http://www.phonetik.phoniatrie.rwth-aachen.de/bkroeger/documents/ipynb_InnerSpeechLoop.zip
100
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4951199A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging.https://github.com/sofroniewn/2pRAM-paper
Loading...
Main menu