F | H | AD | AE | AF | AG | AH | ||
---|---|---|---|---|---|---|---|---|
1 | PMC URL | title | Notebook URL | Code in problem cell | Problem | Comments | License | |
2 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296728 | Diversity 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/PMC3976103 | Software Carpentry: lessons learned. | n/a | |||||
4 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448745 | ActivePapers: a platform for publishing and archiving computer-aided research. | n/a | |||||
5 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278760 | An 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/PMC4267933 | Fast and efficient Drosophila melanogaster gene knock-ins using MiMIC transposons. | n/a | |||||
7 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150318 | Stress-induced mutagenesis and complex adaptation. | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150318/bin/rspb20141025supp2.txt | print "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/PMC4092319 | Enriched 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/PMC3906378 | Powerlaw: 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/PMC4270252 | Perceived displacement explains wolfpack effect. | https://github.com/simkovic/wolfpackRevisited/blob/master/code/Revision1.ipynb | several in https://github.com/simkovic/wolfpackRevisited/tree/master/code | ||||
11 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670004 | CyREST: 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/PMC4559436 | ReproPhylo: An Environment for Reproducible Phylogenomics. | http://nbviewer.jupyter.org/github/HullUni-bioinformatics/ReproPhylo/blob/master/Tutorial_files/Git/Git_Demo.ipynb | |||||
13 | Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases. | n/a | ||||||
14 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355505 | Towards 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/PMC4355505 | Towards 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.ipynb | css_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/PMC4412813 | Orthogonalization 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/PMC4755742 | Planar 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/PMC4496567 | Challenges 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.sh | bash: install-megahit.sh: No such file or directory | |||
19 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658184 | Computing Workflows for Biologists: A Roadmap. | n/a | |||||
20 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631998 | Systems 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.ipynb | from 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/PMC4881760 | Advanced 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.ipynb | multiple notebooks in repo | ||||
22 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379514 | Improving functional magnetic resonance imaging reproducibility. | n/a | |||||
23 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517073 | Lessons 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/PMC4491703 | The number of olfactory stimuli that humans can discriminate is still unknown. | n/a | |||||
25 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528367 | Data 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/PMC4669674 | Tracing 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/PMC4972086 | An 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/PMC5034285 | A 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/PMC5049846 | Integrity 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/PMC4940747 | Tools 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/PMC5014984 | Datathons 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/PMC4946111 | Where next for the reproducibility agenda in computational biology? | ||||||
33 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199146 | The importance of digitized biocollections as a source of trait data and a new VertNet resource. | ||||||
34 | NA | What's What: The (Nearly) Definitive Guide to Reaction Role Assignment. | ||||||
35 | NA | Neurophysiological 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/PMC5145134 | Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. | ||||||
37 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123367 | Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. | ||||||
38 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870738 | Recommendations for open data science. | ||||||
39 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119319 | jicbioimage: a tool for automated and reproducible bioimage analysis. | ||||||
40 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787049 | Systems biology of the structural proteome. | ||||||
41 | NA | Accelerate Healthcare Data Analytics: An Agile Practice to Perform Collaborative and Reproducible Analyses. | ||||||
42 | NA | Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. | ||||||
43 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118469 | Pyrcca: 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/PMC5319736 | Kepler WebView: A Lightweight, Portable Framework for Constructing Real-time Web Interfaces of Scientific Workflows. | ||||||
46 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795700 | Activation of G Proteins by Guanine Nucleotide Exchange Factors Relies on GTPase Activity. | ||||||
47 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868476 | Reticulate evolution is favored in influenza niche switching. | ||||||
48 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5101613 | A public data set of human balance evaluations. | ||||||
49 | NA | An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses. | ||||||
50 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053501 | Language-Agnostic Reproducible Data Analysis Using Literate Programming. | ||||||
51 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054807 | The 2016 Bioinformatics Open Source Conference (BOSC). | ||||||
52 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936733 | A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research. | ||||||
53 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5173344 | Beyond Academia - Interrogating Research Impact in the Research Excellence Framework. | ||||||
54 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720982 | REPRODUCIBLE AND SHAREABLE QUANTIFICATIONS OF PATHOGENICITY. | ||||||
55 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4963212 | Accurate Reconstruction of Cell and Particle Tracks from 3D Live Imaging Data. | ||||||
56 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834562 | PyRhO: A Multiscale Optogenetics Simulation Platform. | ||||||
57 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858870 | High-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/PMC4975741 | A preliminary review of influential works in data-driven discovery. | n/a | |||||
59 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018365 | MEANS: python package for Moment Expansion Approximation, iNference and Simulation. | n/a | |||||
60 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928468 | A 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/PMC5069772 | Avoiding Pandemic Fears in the Subway and Conquering the Platypus. | http://goo.gl/UIhBjf | |||||
62 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5162102 | A 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/PMC4911401 | From 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/PMC5008457 | Real-time selective sequencing using nanopore technology. | https://github.com/mattloose/RUFigs | |||||
65 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5182066 | Accelerated 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/PMC5021153 | From big data to deep insight in developmental science. | n/a | |||||
67 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988647 | FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET. | n/a | |||||
68 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965465 | Dramatic 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/PMC4917969 | Whole-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/PMC5140024 | COMPASS: Continuous Open Mouse Phenotyping of Activity and Sleep Status. | https://github.com/LozRiviera/COMPASS_paper | |||||
71 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739432 | Allergy 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/PMC5019306 | Using 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/PMC5167163 | Evaluating the evaluation of cancer driver genes. | https://github.com/KarchinLab/Tokheim_PNAS_2016 | |||||
74 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817224 | Real-time, portable genome sequencing for Ebola surveillance. | http://github.com/nickloman/ebov | |||||
75 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5095137 | Methods 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/PMC5055122 | Molecular 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/PMC5069741 | Geography 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/PMC4878278 | MIMIC-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/PMC5072699 | Ten Simple Rules for Digital Data Storage. | n/a | |||||
80 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC-7006 | The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination | n/a | |||||
81 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779235 | Bioalerts: 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/PMC4980007 | Preservation 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/PMC5014103 | Geophysical fluid dynamics: whence, whither and why? | n/a | |||||
84 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999233 | Evidence of Online Performance Deterioration in User Sessions on Reddit. | ||||||
85 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4805879 | Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments. | n/a | |||||
86 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890304 | Conservation 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/PMC4884666 | Computational virology: From the inside out. | https://github.com/scipy/scipy/pull/5232 | |||||
88 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986259 | A comprehensive and scalable database search system for metaproteomics. | n/a | |||||
89 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791574 | Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery? | https://github.com/ipython/docker-notebook | |||||
90 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051545 | Finding Our Way in the Dark Proteome. | n/a | |||||
91 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189966 | Experimental 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/PMC4841782 | Brain-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/PMC5069746 | From 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/PMC5158082 | Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus. | n/a | |||||
95 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148610 | Connectivity 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/PMC4941947 | Using 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/PMC5073428 | BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. | n/a | |||||
98 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979073 | Markov 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/PMC4885855 | Modeling 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/PMC4951199 | A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging. | https://github.com/sofroniewn/2pRAM-paper |