75 Matching Annotations
1. May 2018
2. www.pnas.org www.pnas.org
1. backtracking algorithm

Implement this in nipype/niflows

2. MT

Magnetization transfer

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3. www.nature.com www.nature.com
1. Before reproducibility must come preproducibility

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4. www.pnas.org www.pnas.org
1. Adolescence is associated with genomically patternedconsolidation of the hubs of the humanbrain connectome

First repropaper example

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5. group.springernature.com group.springernature.com
1. Researchers’ challenges in sharing data cross geographic borders and disciplines

Another report on challenges in data sharing.

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6. Jan 2018
7. arxiv.org arxiv.org
1. Accurate autocorrelation modeling substantially improvesfMRI reliability

Considering the availability of code and a comparative workflow, this would be a likely candidate for the ReproPaper Initiative.

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8. Sep 2017
9. www.biorxiv.org www.biorxiv.org
1. 10datasetscompris-ing2,295subjectswith2,861scans

perhaps list these are public datasets. i had to look at m2g to figure out.

2. whicharenowpubliclyavailable

Perhaps list m2g.io over here as well.

3. accurate

Since there is no ground truth, how can accuracy be evaluated?

4. slightlyimprovedorsignificantlydeterioratedperformance

How was performance evaluated? Was there an objective method to determine this? Given the different choices of nonlinear registration methods, was ANTs and other tools evaluated.

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10. Aug 2017
11. mbakker7.github.io mbakker7.github.io
1. Exploratory computing with Python

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12. github.com github.com
1. Gallery

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13. www.interaction-design.org www.interaction-design.org
1. The Properties of Human Memory and Their Importance for Information Visualization

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14. www.informationisbeautiful.net www.informationisbeautiful.net

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15. journal.frontiersin.org journal.frontiersin.org
1. When Null Hypothesis Significance Testing Is Unsuitable for Research: A Reassessment

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16. Jan 2017
17. www.nature.com www.nature.com
1. Replication studies offer much more than technical details

Another editorial highlighting that highlights the merits of replication beyond repeat and raises questions about the culture of science and confirmation bias.

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18. Nov 2016
19. stepik.org stepik.org
1. We are open for knowledge

just came across this platform. It's used in PyCharm to provide Python tutorial functionality.

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20. www.w3.org www.w3.org
1. Data on the Web Best Practices

A description for different qualities and targets for data sharing or publishing.

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21. samnicholls.net samnicholls.net
1. Bioinformatics is a disorganised disaster and I am too. So I made a shell.

This is a shell-wrapper to minimize the effort needed to collect command line provenance.

This post covers a lot of ground to describe practical and human requirements.

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22. www.software.ac.uk www.software.ac.uk
1. Top ten reasons to not share your code (and why you should anyway)

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23. Oct 2016
1. Linked Data: Evolving the Web into a Global Data Space

A comprehensive book on linked data.

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25. www.datacarpentry.org www.datacarpentry.org
1. Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research.

Training for data skills

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26. www.wings-workflows.org www.wings-workflows.org
1. WINGS is a semantic workflow system

A meta level representation of workflows.

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27. Sep 2016
28. www.pachyderm.io www.pachyderm.io
1. A Containerized Data Lake

A data container + workflow spec

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29. github.com github.com
1. duecredit/duecredit

A Python library to include citations in your python software packages.

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30. aws.amazon.com aws.amazon.com
1. CfnCluster

Amazon's own product similar to starcluster.

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31. dataverse.harvard.edu dataverse.harvard.edu
1. Brain Genomics Superstruct Project (GSP)

License: Data use agreement Access: Human, API Needs data use agreement: Yes Needs institutional signature for access: No

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32. studyforrest.org studyforrest.org
1. What is studyforrest?

Rich multimodal dataset on naturalistic stimuli

• Access: Human, rsync, git annex
• Needs data use agreement: No
• Needs institutional signature for access: No

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33. Aug 2016
34. fivethirtyeight.com fivethirtyeight.com
1. Science Isn’t Broken

A nice tool that illustrates the impact of being able to continuously run tests.

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35. journals.plos.org journals.plos.org
1. Ten Simple Rules for Effective Statistical Practice

A very nice overview of things to keep in mind when designing experiments and analyzing data with statistics

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36. garstats.wordpress.com garstats.wordpress.com
1. Robust effect sizes for 2 independent groups

A nice treatise on how to measure effect sizes robustly

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37. fivethirtyeight.com fivethirtyeight.com
1. Not Even Scientists Can Easily Explain P-values

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38. library.mpib-berlin.mpg.de library.mpib-berlin.mpg.de
1. Th e Null Ritual What You Always Wanted to Know About Signifi cance Testing but Were Afraid to Ask

Understanding null hypothesis testing and considering alternatives

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39. neurohackweek.github.io neurohackweek.github.io
1. Lesson template for Neurohackweek

A GitHub template for creating lesson plans. While this doesn't provide the flexibility of a computational environment within this lesson plan, it serves as a good approach to outline concepts of lessons.

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40. www.nature.com www.nature.com
1. replication ecosystem, such as it is, lacks visibility, value and conventions.

a key social concern

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41. www.kaggle.com www.kaggle.com
1. Welcome to Kaggle Datasets

Kaggle now allows publish datasets. It will be interesting to investigate what kind of datasets are allowed and how it captures metadata.

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42. waffle.io waffle.io
1. Smart & Simple Project Management

another project management solution for GitHub and it appears to be free. i may replace zenhub with this.

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43. Jul 2016
44. nautil.us nautil.us
1. We Should Not Accept Scientific Results That Have Not Been Repeated

A nice article on reproducibility and need for structural change in science.

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45. dat-data.com dat-data.com
1. The Dat Project

A peer-to-peer data distribution service

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46. learningequality.org learningequality.org
1. An offline version of Khan Academy.

A lightweight deployable platform for teaching from khan academy.

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47. www.cambridgesemantics.com www.cambridgesemantics.com
1. A beginner's introduction to Semantic Web and Linked Data.

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48. osf.io osf.io
1. Openness is a core value of scientific practice.

A set of badges to tag open science.

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49. try.github.io try.github.io
1. Got 15 minutes and want to learn Git?

A tutorial from GitHub to learn git.

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50. Jun 2016
51. www.nih.gov www.nih.gov
1. Training

NIH efforts towards reproducibility. This includes videos for training and discussion material as well.

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52. cds.nyu.edu cds.nyu.edu
1. ReproZip

a python framework for packaging experiments for publication

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53. rr-project.org rr-project.org
1. rr

record and replay application

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54. bitbucket.org bitbucket.org
1. smtp: mail.server

this doesn't matter

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55. May 2016
1. Easily deploy applications at any scale

A modern distributed scheduler

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57. www.nature.com www.nature.com
1. Reality check on reproducibility

Survey about the state of reproducibility

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1. Course Builder

tool to create courses

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59. www.zenhub.io www.zenhub.io
1. Manage projects without leaving GitHub.

another trello like project management system integrated with github.

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60. wekan.io wekan.io
1. The open-source Trello-like kanban

opensource trello like platform

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61. sandstorm.io sandstorm.io
1. Sandstorm

an opensource framework for app distribution. list of apps at:

https://apps.sandstorm.io/

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62. bitesizebio.com bitesizebio.com
1. this is relevant to training

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63. Feb 2016
64. github.com github.com
1. the ants registration can be made more robust by removing the Translate transform and using use initial_moving transform. i do like the transform parameters here:

https://github.com/nipy/nipype/blob/master/examples/fmri_ants_openfmri.py#L202

2. datasource can be combined into a single datagrabber. along the lines here: https://github.com/nipy/nipype/blob/master/examples/fmri_ants_openfmri.py#L667

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65. Jun 2014
66. github.com github.com
1. our

Our

2. For example, slicing a set of ordered series data by rows (spectral dimension) and columns (temporal dimension) is quite simple:

This is indeed a simple example. However, could you provide a few non-trivial use cases that are made really simple?

3. Top: Absorbance

These figures are also missing axes labels.

4. The simulation codebase may be found

Include this link in the abstract/introduction.

5. Temporal evolution

Figures have no labeling on the axes.

6. relevant plasmonic

relevant to plasmonic

7. Despite these benefits, nanobiosensing research in general is faced with several hinderances.

Despite these benefits, several issues impede nanobiosensing research.

8. A Computational Framework for Plasmonic Nanobiosensing

Quality of the approach: meets Quality of the writing: meets Quality of the figures/tables: below

Is the code made publicly available and does the article sufficiently describe how to access it?

yes

Does the article present the problem in an appropriate context? Specifically, does it:

• explain why the problem is important --> yes
• describe in which situations it arises --> yes outline relevant previous work -> cannot judge provide background information for non-experts -> yes

Is the content of the paper accessible to a computational scientist with no specific knowledge in the given field?

the article does provide some background that made it easier for me to follow, but i simply do not have expertise in the underlying domain.

Does the paper describe a well-formulated scientific or technical achievement?

appears to.

Are the technical and scientific decisions well-motivated and clearly explained? Are the code examples (if any) sound, clear, and well-written?

these are primarily driven by the need for a simple way to interact with the sensors.

Is the paper factual correct? Is the language and grammar of sufficient quality?

there are a few typos that i have noted, but otherwise yes.

Are the conclusions justified?

yes - from the perspective of simplicity.

Is prior work properly and fully cited?

i cannot comment on this.

Should any part of the article be shortened or expanded? Please explain. In your view, is the paper fit for publication in the conference proceedings? Please suggest specific improvements and indicate whether you think the article needs a significant rewrite (rather than a minor revision).

yes

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67. github.com github.com
1. amg_cycle

docstring - also use of exec is not recommended. please expand parameters into keyword args.

2. iterative_solve

docsting

3. coarsen_A(

docstring

4. def restriction(N, shape):

5. restrictions

missing docstring here

6. coarse point nearest to the camera in the bottom

perhaps indicate this explicitly in the figure

7. OpenMG: A New Multigrid Implementation in Python

Quality of the approach: meets Quality of the writing: meets Quality of the figures/tables: meets

Is the code made publicly available and does the article sufficiently describe how to access it? yes

Does the article present the problem in an appropriate context? Specifically, does it:

• explain why the problem is important --> yes
• describe in which situations it arises --> yes
• outline relevant previous work -> some, cannot judge full extent
• provide background information for non-experts -> yes

Is the content of the paper accessible to a computational scientist with no specific knowledge in the given field?

the article does provide some background that made it easier for me to follow, but i do not have sufficient expertise in Galerkin discretization approaches, but the general idea of using multi resolution solvers to iteratively approximate the true solution was conveyed in the article.

Does the paper describe a well-formulated scientific or technical achievement?

yes

Are the technical and scientific decisions well-motivated and clearly explained? Are the code examples (if any) sound, clear, and well-written?

yes. the code examples can be improved with better Python standards as noted.

Is the paper factual correct? Is the language and grammar of sufficient quality? Are the conclusions justified?

yes

Is prior work properly and fully cited?

i cannot comment on this.

Should any part of the article be shortened or expanded? Please explain. In your view, is the paper fit for publication in the conference proceedings? Please suggest specific improvements and indicate whether you think the article needs a significant rewrite (rather than a minor revision).

yes

8. OpenMG

include URL here

9. overall accuracy

how is accuracy evaluated? is it simply || Au^\hat - b ||_2?

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68. web.hypothes.is web.hypothes.is
1. Imagine

showing a demo of hypthesis at brainhack

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69. Feb 2014
70. brainspell.org brainspell.org