From 764f4a8b045007c74ff41ea60352cd92259df375 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 10:25:22 -0500 Subject: [PATCH 01/10] Edit and style front page --- content/_index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/content/_index.md b/content/_index.md index 5f2df94..8f8812f 100644 --- a/content/_index.md +++ b/content/_index.md @@ -20,13 +20,13 @@ To deliver effective tools, training, and principles to the neuroimaging communi link="/resources/getting-started/" title="Getting Started" image="/images/sec-started2.webp" - subtitle="Getting Started with ReproNim" + subtitle="Getting started with ReproNim" >}} {{< rn-button link="/resources/tools/" title="Tools" image="/images/tools.webp" - subtitle="ReproNim Tools" + subtitle="ReproNim tools" >}} {{< rn-button link="/fellowship/" @@ -38,6 +38,6 @@ To deliver effective tools, training, and principles to the neuroimaging communi link="/about/why/" title="Why" image="/images/sec-why2.webp" - subtitle="Why Reproducible Neuroimaging" + subtitle="Why reproducible neuroimaging" >}} {{< /rn-buttons >}} From 5e532e17c2b0aa7293249a44bc110076ed47f668 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 10:46:39 -0500 Subject: [PATCH 02/10] Edit and style About page --- content/about/_index.md | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/content/about/_index.md b/content/about/_index.md index 51f9801..f1f6713 100644 --- a/content/about/_index.md +++ b/content/about/_index.md @@ -3,31 +3,33 @@ title: About type: docs --- -ReproNim is a national multi-site technology and research development Center for reproducible neuroimaging computation, funded by a P41 award from the National Institute of Biomedical Imaging and Bioengineering. +ReproNim is a national multi-site technology and research development center for reproducible neuroimaging computation. ReproNim is funded by a [P41 award](https://reporter.nih.gov/project-details/8999833#description) from the [National Institute of Biomedical Imaging and Bioengineering](https://www.nibib.nih.gov/). -Collectively, our project and core teams are based across six sites (UMass Chan Medical School, MIT, Dartmouth College, McGill, UCSD, and UCI) in North America. +Our project and core teams are based at six sites: UMass Chan Medical School, MIT, Dartmouth College, McGill University, The University of California San Diego, and UC Irvine. ## What we do -Our mission is to enhance reproducibility of neuroimaging research by developing, disseminating and spurring adoption of key concepts, practices and tools. +ReproNim's mission is to deliver effective tools, training, and principles to the neuroimaging community to support the entire neuroimaging workflow for rigorous, reproducible, and FAIR neuroimaging. ## What we offer -ReproNim offers a variety of resources to educate and enable individual researchers, imaging centers and students on both conceptual and practical fundamentals of reproducible neuroimaging, why it is important and how to do it through principles, tools and training. +ReproNim offers a variety of resources to educate and enable individual researchers, imaging centers, and students. Our resources address both conceptual and practical fundamentals of reproducible neuroimaging, why it is important, and how to do it through principles, tools, and training. ## ReproNim/INCF Fellows -The ReproNim/INCF Fellows (33 graduates, and 12 current fellows) are an important extension of ReproNim, with international representation and educational reach to highly varied audiences encompassing all career stages and diverse resources. -The ReproNim/INCF Fellowship is a full year, project-based Train-the-Trainer program, with access to networking and mentorship in support of Fellows' training program development endeavors, which are tailored to their respective target audiences, training objectives, and local environs. -The program is open by competitive review, to applicants at all career stages. +The [ReproNim/INCF Fellowship](/fellowship/) is a full year, project-based train-the-trainer program with access to networking and mentorship. It supports Fellows' training program development endeavors, which are tailored to their respective target audiences, training objectives, and local environs. -## Join the ReproNim Community +[ReproNim/INCF Fellows](/fellowship/#2024-awardees) (33 graduates, and 12 current fellows) are an important extension of ReproNim, with international representation and educational reach to highly varied audiences encompassing all career stages and diverse resources. -- Sign up for our [mailing list](https://www.nitrc.org/mailman/listinfo/repronim-announcement) - - Follow our [webinar series](https://www.youtube.com/channel/UCGX2sXmEgDuUGWHDSiT1NdQ/videos) - - Read [The ReproNim Blog](https://reprodev.wordpress.com/category/article/) - - [Become a Fellow](/fellowship) +The program is open by competitive review to applicants at all career stages. + +## Join the ReproNim community + +- Sign up for our [mailing list](https://www.nitrc.org/mailman/listinfo/repronim-announcement). + - Follow our [webinar series](https://www.youtube.com/channel/UCGX2sXmEgDuUGWHDSiT1NdQ/videos). + - Read [The ReproNim Blog](https://reprodev.wordpress.com/category/article/). + - [Become a Fellow](/fellowship/). ## Contact us -Email us at . +Email us at info@repronim.org. From 0b9ccb05a6e4ce2462da42086e0aef70fd8dd686 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 10:52:15 -0500 Subject: [PATCH 03/10] Edit and style team page --- content/about/team.md | 52 +++++++++++++++++++++---------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/content/about/team.md b/content/about/team.md index e20252e..d92481b 100644 --- a/content/about/team.md +++ b/content/about/team.md @@ -1,11 +1,11 @@ --- -title: Meet the ReproNim Team! +title: Meet the ReproNim Team linkTitle: ReproNim Team type: docs weight: 10 --- -## ReproNim Leadership +## ReproNim leadership - [David Kennedy](https://profiles.umassmed.edu/display/130002) ReproNim PI - ReproNim: A Center for Reproducible Neuroimaging Computation - Professor of Psychiatry and Radiology, UMass Chan Medical School, Worcester, MA @@ -15,7 +15,7 @@ weight: 10 - [Maryann Martone](https://profiles.ucsd.edu/maryann.martone) Project 1 Co-Lead - A FAIR Data and Metadata Foundation for Reproducible Research (DISCOVER) - Professor Emerita of Neuroscience, UC San Diego Health Sciences, San Diego, CA - Principal Investigator, [FAIR Data Informatics Lab](https://www.fdilab.org/team) at UCSD - - Chair, Governing Board, [INCF](https://www.incf.org/team/prof-maryann-martone) + - Former Chair, Governing Board, INCF - [Jeffrey Grethe](https://profiles.ucsd.edu/jeffrey.grethe) Project 1 Co-Lead - A FAIR Data and Metadata Foundation for Reproducible Research (DISCOVER) - Associate Director, Neurosciences, UC San Diego Health Sciences, San Diego, CA - Principal Investigator, [FAIR Data Informatics Lab](https://www.fdilab.org/team) at UCSD @@ -37,43 +37,43 @@ weight: 10 ## Full team - University of Massachusetts Chan Medical School, Worcester, MA - - David Kennedy Principal Investigator - - Julie Bates Administrative Core - - Christian Haselgrove Senior Software Engineer - - Steven Hodge Data Analyst, Statistician + - David Kennedy, Principal Investigator + - Julie Bates, Administrative Core + - Christian Haselgrove, Senior Software Engineer + - Steven Hodge, Data Analyst and Statistician - Massachusetts Institute of Technology, Cambridge, MA - - Satra Ghosh Project Lead - - Yibei Chen Postdoctoral Researcher - - Tek Raj Chhetri Postdoctoral Researcher - - Dorota Jarecka Research Scientist + - Satra Ghosh, Project Lead + - Yibei Chen, Postdoctoral Researcher + - Tek Raj Chhetri, Postdoctoral Researcher + - Dorota Jarecka, Research Scientist - Dartmouth College, Hanover, NH - - Yaroslav Halchenko Project Lead - - Austin Macdonald Scientific Software Developer - - Vadim Melnick Scientific Software Developer, Consultant - - Isaac To Scientific Software Developer + - Yaroslav Halchenko, Project Lead + - Austin Macdonald, Scientific Software Developer + - Vadim Melnick, Scientific Software Developer, Consultant + - Isaac To, Scientific Software Developer - McGill University, Montreal, Canada - - Jean-Baptise Poline Project Lead - - Alyssa Dai Developer - - Arman Jahanpour Developer - - Brent McPherson Postdoctoral Researcher - - Sebastian Urchs Senior Scientific Software Developer + - Jean-Baptise Poline, Project Lead + - Alyssa Dai, Developer + - Arman Jahanpour, Developer + - Brent McPherson, Postdoctoral Researcher + - Sebastian Urchs, Senior Scientific Software Developer - University of California at Irvine, Irvine, CA - - David Keator Senior Investigator + - David Keator, Senior Investigator - University of California at San Diego, San Diego, CA - - Maryann Martone and Jeff Grethe Project Leads - - Sean Hatton Research Data Analyst - - Fahim Imam Assistant Project Scientist + - Maryann Martone and Jeff Grethe, Project Leads + - Sean Hatton, Research Data Analyst + - Fahim Imam, Assistant Project Scientist - Preuss Enterprises, Inc. - - Nina Preuss Investigator + - Nina Preuss, Investigator ## Directory -ReproNim Alumni are indicated by asterisks. +ReproNim alumni are indicated by asterisks. {{< people "repronim-team" >}} From b1eb995c1dc30a56e3996d47be7ca8e0930262af Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 10:54:10 -0500 Subject: [PATCH 04/10] Edit and style EAB page --- content/about/eab.md | 1 - 1 file changed, 1 deletion(-) diff --git a/content/about/eab.md b/content/about/eab.md index fbc45ec..e6a12eb 100644 --- a/content/about/eab.md +++ b/content/about/eab.md @@ -15,7 +15,6 @@ weight: 20 - Christina L. Williams Professor of Neuroscience - Department of Neuroscience and Behavior - Barnard College, New York NY - - BJ's previous lab website: FabLab at Yale - [Member, American Academy of Arts & Sciences](https://www.amacad.org/person/bj-casey) - [Damien Fair, PhD](https://midb.umn.edu/staff/damien-fair) From ac9b28b658d7a803853b7bfd994b5afdf3be6424 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 11:04:33 -0500 Subject: [PATCH 05/10] Edit and style collaborators page --- content/about/collaborators.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/content/about/collaborators.md b/content/about/collaborators.md index f62585b..37d0e9a 100644 --- a/content/about/collaborators.md +++ b/content/about/collaborators.md @@ -4,9 +4,9 @@ type: docs weight: 30 --- -Our efforts are substantially informed and enhanced through the breadth and depth of scientific expertise of our collaborative liaisons, including both [Collaborating Projects](/about/collaborators/#collaborating-projects) and Service Projects. +Our efforts are substantially informed and enhanced through the breadth and depth of scientific expertise of our collaborators in both [Collaborating Projects](#collaborating-projects) and [Service Projects](#service-projects). -[Contact us](mailto:info@repronim.org) if you are interested in becoming a ReproNim Collaborating or Service Project +[Contact us](mailto:info@repronim.org) if you are interested in becoming a ReproNim Collaborating or Service Project.
@@ -44,7 +44,7 @@ Our efforts are substantially informed and enhanced through the breadth and dept We are collaborating with numerous groups around the country and abroad to synergistically develop ReproNim tools in concert with (and as informed by) rapidly advancing technologies in a variety of areas including image analysis, workflow processing, data sourcing and hosting, and associated API developments. -The P41 Center Collaborative Projects (CPs) serve as technology drivers, users, and testbeds for the cutting-edge technology developed in Technology, Research and Development projects. +The P41 Center Collaborative Projects (CPs) serve as technology drivers, users, and testbeds for the cutting-edge technology developed in P41 Technology, Research and Development projects. - CP1: [Segmenting Brain Structures for Neurological Disorders](https://reporter.nih.gov/search/kT7X-zyN302C6XNNo4g5xQ/project-details/10295766) - [Bruce Fischl](https://www.nmr.mgh.harvard.edu/user/5499) (PI) @@ -56,13 +56,13 @@ The P41 Center Collaborative Projects (CPs) serve as technology drivers, users, - [Alan Evans](https://mcin.ca/about-mcin/alans-cv/) (PI) - Institution: McGill University - CP4: [COINSTAC: Worldwide Analysis of Valence System Brain Circuits](https://coinstac.org/) - - [Vince Calhoun](https://www.ece.gatech.edu/faculty-staff-directory/vince-calhoun), [Jessica Turner](https://trendscenter.org/jessica-turner/), [Theodorus Van Erp](https://www.faculty.uci.edu/profile.cfm?faculty_id=5812) (PIs) + - Vince Calhoun, [Jessica Turner](https://trendscenter.org/jessica-turner/), [Theodorus Van Erp](https://www.faculty.uci.edu/profile.cfm?faculty_id=5812) (PIs) - Institutions: Georgia State University/UC Irvine - CP5: [OpenNeuro: An Open Archive for Analysis and Sharing of Brain Initiative Data](https://openneuro.org/) - [Russell Poldrack](https://profiles.stanford.edu/russell-poldrack) (PI) - Institution: Stanford University - CP6: [Brainlife: Lowering the Barrier of Entry to Network Neuroscience](https://brainlife.io/about/) - - [Franco Pestilli](https://cns.utexas.edu/directory/item/66-other/4455-pestilli-franco?Itemid=349) (PI) + - Franco Pestilli (PI) - Institution: University of Texas at Austin - CP7: [DataLad: Versatile Platform for Digital Logistics](https://www.datalad.org/) - [Michael Hanke](https://www.psychoinformatics.de/lab-members.html) (PI) @@ -92,7 +92,7 @@ The P41 Center provides their technology to Service Projects (SPs) that serve as - SP3: [Neuroscience Gateway to Enable Dissemination of Computational and Data Processing Tools and Software](https://www.nsgportal.org/overview.html) - [Amitava Majumdar](https://www.sdsc.edu/~majumdar/) and [Kenneth Yoshimoto](https://www.sdsc.edu/research/researcher_spotlight/yoshimoto_kenneth.html) and [Subhashini Sivagnanam](https://users.sdsc.edu/~sivagnan/) (PIs) - Institution: University of California at San Diego -- SP4: [CRCNS: NeuroBridge: Connecting Big Data for Reproducible Clinical Neuroscience](https://neurobridges.org/about.html) +- SP4: [CRCNS: NeuroBridge: Connecting Big Data for Reproducible Clinical Neuroscience](https://neurobridges.org/) - [Lei Wang](https://medicine.osu.edu/find-faculty/clinical/psychiatry-and-behavioral-health/lei-wang-phd) (PI) - Institution: Ohio State University - SP5: [EAGER: Community Building and Workflows for Data Sharing with Publicly Accessible and Consumable Metadata](https://www.linknovate.com/grant/eager-community-building-and-workflows-for-data-sharing-with-publicly-accessible-and-consumable-metadata-317869/) From c636309db43c3722ada0d81108cd7e062347d732 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 11:09:56 -0500 Subject: [PATCH 06/10] Edit and style webinar page --- content/about/webinars.md | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/content/about/webinars.md b/content/about/webinars.md index 68d766a..dd40658 100644 --- a/content/about/webinars.md +++ b/content/about/webinars.md @@ -5,19 +5,17 @@ type: docs weight: 50 --- -Introducing Important Efforts in Reproducibility, featuring presentations by both ReproNim and Guest Investigators. +The ReproNim webinar series introduces important efforts in reproducibility featuring presentations by both ReproNim and guest investigators. -Browse our complete collections of ReproNim Webinar -[Videos](https://www.youtube.com/channel/UCGX2sXmEgDuUGWHDSiT1NdQ/videos) and -[Slides](https://drive.google.com/drive/folders/1xqgWtghspJtxa8hmC4d6_zUPCgpe4fp-) +Browse our complete collections of ReproNim webinar [videos](https://www.youtube.com/channel/UCGX2sXmEgDuUGWHDSiT1NdQ/videos) and [slides](https://drive.google.com/drive/folders/1xqgWtghspJtxa8hmC4d6_zUPCgpe4fp-). -## Upcoming Webinars +## Upcoming webinars ### Friday, January 3, 2025 No Webinar ~ Happy New Year! -## Webinar Presentations to Date +## Webinar presentations to date ### Friday, December 6, 2024 at 2pm EST Our featured speaker this month is ReproNim/INCF Fellowship alum [Johanna Bayer](https://nl.linkedin.com/in/johanna-bayer) who joins us from the [Predictive Clinical Neuroscience Group](https://predictiveclinicalneuroscience.com/),(Donders Institute and RadboudUMC, Netherlands). Johanna discusses normative modeling of neuroimaging data using the Predictive Clinical Neuroscience toolkit ([pcntoolkit](https://pcntoolkit.readthedocs.io/en/latest/)), in her presentation: "Normative modelling using the pcntoolkit – the what when and why.” @@ -41,7 +39,7 @@ Chris has very considerable expertise in large systems-level computation modelin [Video Presentation](https://youtu.be/pH4hiUaknow) is now available -### Summer Hiatus ~ July-August 2024 +### Summer hiatus ~ July-August 2024 ### Friday, June 7, 2024 ReproNim faculty member [Yaroslav Halchenko](https://pbs.dartmouth.edu/people/yaroslav-o-halchenko-0) discusses principles, methods, and automation for the scientific operations in reproducible neuroimaging experiments in: "SciOps from ReproNim/ReproFlow." @@ -85,7 +83,7 @@ We welcome [Anisha Keshavan](https://theorg.com/org/octave-bioscience/org-chart/ [Video Presentation](https://youtu.be/NTl-25tgKgY) and [Slides](http://fnndsc.childrens.harvard.edu/ChRIS/ReproNim) are now available. -### July-September, 2023 ~ Summer Hiatus +### July-September, 2023 ~ summer hiatus ### Friday, June 2, 2023 at 2pm EDT [Arno Klein](https://matter.childmind.org/) is our special guest speaker, joining us from the Child Mind Institute to share some of his intriguing and innovative technological developments aimed at better understanding of and treatment for childhood mental health disorders: [MindLogger platform](https://mindlogger.org/) for configurable data collection and interventions in research and clinical practice @@ -136,7 +134,7 @@ We kick off the new academic year with a special presentation by ReproNim facult [Video Presentation](https://youtu.be/hX_JnsZz-uY) is now available. -### Summer Hiatus, Friday July 1 - Friday September 2, 2022 +### Summer hiatus, Friday July 1 - Friday September 2, 2022 ### Friday, June 3, 2022 at 2pm EDT Special guest speaker [Ted Satterthwaite](https://www.pennlinc.io//team/Ted-Satterthwaite) joins us from UPenn's [Lifespan Informatics and Neuroimaging Center](https://www.pennlinc.io/research), with a presentation on Reproducible Image Curation and Processing for Large-scale Studies of Brain Development. @@ -256,7 +254,7 @@ ReproNim investigator Satra Ghosh addresses the topic of "Harmonizing clinical a [Video Presentation](https://youtu.be/dDuP-Znso5Y) and [Slides](https://docs.google.com/presentation/d/1H4C_cBU9BE9EYFNyK8YBLQObzvq9iDztLWrqRIQTmgc/edit#slide=id.p) are now available. -### Friday, July 3, 2020 ~~No Meeting~~ Happy Summer! +### Friday, July 3, 2020 ~ no meeting ~ happy summer! ### Friday, June 5, 2020 at 2pm EDT ReproNim investigator Yaroslav Halchenko presents "Version control your data and computation using containers, DataLad and ReproMan, and reproducible they be!" From 1a5eeae0bf371859af3f4a0ed3451fc72a9cdfe3 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 11:23:07 -0500 Subject: [PATCH 07/10] Further edit/style collaborators --- content/about/collaborators.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/about/collaborators.md b/content/about/collaborators.md index 37d0e9a..fdc82f9 100644 --- a/content/about/collaborators.md +++ b/content/about/collaborators.md @@ -87,7 +87,7 @@ The P41 Center provides their technology to Service Projects (SPs) that serve as - [Susan Bookheimer](https://www.semel.ucla.edu/autism/team/susan-bookheimer-phd) (PI) - Institution: University of California at Los Angeles - SP2: [Environment, Epigenetics, Neurodevelopment & Health of Extremely Preterm Children](https://elgan.fpg.unc.edu/) - - [Michael O’Shea](https://www.med.unc.edu/childrensresearch/directory/michael-oshea-md-mph/) and [Rebecca Fry](https://sph.unc.edu/adv_profile/rebecca-fry-phd/) (PIs) + - [Michael O'Shea](https://www.med.unc.edu/childrensresearch/directory/michael-oshea-md-mph/) and [Rebecca Fry](https://sph.unc.edu/adv_profile/rebecca-fry-phd/) (PIs) - Institution:University of North Carolina at Chapel Hill - SP3: [Neuroscience Gateway to Enable Dissemination of Computational and Data Processing Tools and Software](https://www.nsgportal.org/overview.html) - [Amitava Majumdar](https://www.sdsc.edu/~majumdar/) and [Kenneth Yoshimoto](https://www.sdsc.edu/research/researcher_spotlight/yoshimoto_kenneth.html) and [Subhashini Sivagnanam](https://users.sdsc.edu/~sivagnan/) (PIs) From d568e6825cb80c76d7fcf20ed7751c96a6dc07c5 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 11:30:07 -0500 Subject: [PATCH 08/10] Edit and style Why page --- content/about/why.md | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/content/about/why.md b/content/about/why.md index 3e97e72..5536006 100644 --- a/content/about/why.md +++ b/content/about/why.md @@ -4,27 +4,27 @@ type: docs weight: 70 --- -Neuroimaging, like many fields of science, has been described as having a “reproducibility crisis”. We most often hear about this crisis in the context of trust in science and the ability to reproduce the results of studies published by others. It is, of course, frustrating when you waste time and resources on trying to replicate others’ research only to find that the experiment failed. We know that some of the causes of the current reproducibility crisis are poor study design, including underpowered studies. But it is also true that even in a properly designed neuroimaging study, more and more evidence has emerged that any set of results is very sensitive to even small variations in computational environments, preprocessing steps, statistical models and analyses used. In fact, as we state in our [2019 paper](https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2019.00001/full), when it comes to reproducibility in neuroimaging, “Everything matters”. +Neuroimaging, like many fields of science, has been described as having a "reproducibility crisis." We most often hear about this crisis in the context of trust in science and the ability to reproduce the results of studies published by others. It is, of course, frustrating when you waste time and resources trying to replicate others' research only to find that the experiment failed. We know that some of the causes of the current reproducibility crisis are poor study design, including underpowered studies. But it is also true that even in a properly designed neuroimaging study, more and more evidence has emerged that any set of results is very sensitive to even small variations in computational environments, preprocessing steps, statistical models, and analyses used. In fact, as we state in our [2019 paper](https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2019.00001/full), when it comes to reproducibility in neuroimaging, "everything matters." -Reproducible neuroimaging is therefore not only a concern to those outside your lab trying to build on your work, but to you as a researcher, project director or principal investigator. Can you reproduce your own research? Can your graduate students? Can your present and future post-docs? If a reviewer asks you to perform a different analysis on the same data, can you? +Reproducible neuroimaging is therefore not only a concern to those outside your lab trying to build on your work, but to you as a researcher, project director, or principal investigator. Can you reproduce your own research? Can your graduate students? Can your present and future post-docs? If a reviewer asks you to perform a different analysis on the same data, can you? -## What is Reproducible Neuroimaging? +## What is reproducible neuroimaging? ### Scientific reproducibility -First, what do we mean when we say that scientific results are reproducible? Reproducibility is a broad term and is often used as a generic term to refer to replicate at some level the findings of a study. Here, we use the term scientific reproducibility in general to mean **re-executability**, that is, the ability to obtain the exact same results when the same data is analyzed using the exact same analysis methods. Re-executability focuses on methodological reproducibility and should be seen as simply the first step in establishing the validity of a given set of results. A **result**, that is, a claim made about the meaning of a study, is fully reproducible when it can be **re-executed** and **generalized** independently. Some of what we are referring to as generalization is referred to as **replication**, defined as repeating an entire study with new data to see if the original results can be replicated. But as you can see in the graphic below, there are multiple types of replication in the age of open data and tool sharing. A true biological inference should hold true regardless of the methods used to observe a biological process or the specific sample of the population being studied. +First, what do we mean when we say that scientific results are reproducible? _Reproducibility_ is a broad term and is often used casually to mean the replication of the findings of a study at some level. Here, we use the term _scientific reproducibility_ in general to mean _re-executability_, the ability to obtain the exact same results when the same data is analyzed using the exact same analysis methods. Re-executability focuses on methodological reproducibility and should be seen as simply the first step in establishing the validity of a given set of results. A _result_, a claim made about the meaning of a study, is fully reproducible when it can be re-executed and generalized independently. Some of what we are referring to as generalization is referred to as _replication_, defined as repeating an entire study with new data to see if the original results can be replicated. But as you can see in the graphic below, there are multiple types of replication in the age of open data and tool sharing. A true biological inference should hold true regardless of the methods used to observe a biological process or the specific sample of the population being studied. ![image](/images/spectrum.png) -### Reproducible Neuroimaging +### Reproducible neuroimaging -Building on the materials above, reproducible neuroimaging refers to the practice of conducting and disseminating neuroimaging research in a manner that allows others to independently verify and replicate the findings. It encompasses a set of principles, practices, and tools aimed at ensuring transparency, rigor, and accountability in neuroimaging studies. Transparency is achieved through others **being able to know** **precisely *‘what operations’* were performed on *‘what data’*** . Remember, the “others” that benefit from reproducible neuroimaging include: +Building on the materials above, reproducible neuroimaging refers to the practice of conducting and disseminating neuroimaging research in a manner that allows others to independently verify and replicate the findings. It encompasses a set of principles, practices, and tools aimed at ensuring transparency, rigor, and accountability in neuroimaging studies. Transparency is achieved through others being able to know precisely what operations were performed on what data. Remember, the "others" that benefit from reproducible neuroimaging include: -* You -* Future you -* Your lab -* Your colleagues -* Reviewers -* Other neuroimagers -* Data scientists -* AI +* you, +* future you, +* your lab, +* your colleagues, +* reviewers, +* other neuroimagers, +* data scientists, and +* AI. From 860aa8bbf2d5de5733c88c32031620c8414a49c5 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 12:10:14 -0500 Subject: [PATCH 09/10] Edit and style In Practice" page --- content/about/in-practice.md | 122 +++++++++++------- .../resources/tutorials/data-dictionary.md | 2 +- content/resources/tutorials/dicom-to-bids.md | 2 +- content/resources/tutorials/git.md | 2 +- content/resources/tutorials/nipoppy.md | 2 +- content/resources/tutorials/pond-lake.md | 2 +- .../resources/tutorials/publish-everything.md | 2 +- .../tutorials/repronim-containers.md | 2 +- content/resources/tutorials/reproschema.md | 2 +- 9 files changed, 85 insertions(+), 53 deletions(-) diff --git a/content/about/in-practice.md b/content/about/in-practice.md index 710749d..4e6e974 100644 --- a/content/about/in-practice.md +++ b/content/about/in-practice.md @@ -7,10 +7,10 @@ weight: 80 ## ReproNim's principles of reproducible neuroimaging @@ -18,48 +18,80 @@ references to them (by NUMBER.LETTER) on other pages. ol ol li { list-style-type: lower-alpha; } -1. Study planning: - 1. Implement good science basics, e.g., power analysis, statistical consult - 2. Consider using pre-existing data for planning and/or analysis - 3. Create an [NIH-compliant data management and sharing plan](https://sharing.nih.gov/data-management-and-sharing-policy/planning-and-budgeting-for-data-management-and-sharing/writing-a-data-management-and-sharing-plan#after) - 4. Adopt [open consent](https://open-brain-consent.readthedocs.io/en/stable/) to allow broad sharing of data - 5. [Pre-register](https://www.cos.io/initiatives/prereg) your study - -1. Data and metadata management: - 1. Use **standard** data formats and extend them to meet your needs. - 2. Use **version control** from start to finish - 3. **Annotate** data using standard, reproducible procedures - -1. Software management: - 1. Use released versions of open source software tools. - 2. Use **version control** from start to finish - 3. Automate the installation of your code and its dependencies - 4. Automate the execution of your data analysis - 5. **Annotate** your code and workflows using standard, reproducible procedures - 6. Use **containers** where reasonable - -1. Publishing everything: publishing re-executable publications - 1. Plans should be shared (pre-registration) - 2. Software should be shared - 3. Data should be shared - 4. All research objects should be FAIR - -In turn, as indicated by the blue highlights in the above figure, **four core actions** are key to implementing these principles: - -## ReproNim's 4 Core Actions - -1) **Use of Standards:** Using standard data formats and extending them to meet specific research needs is important for *data and metadata management* in reproducible neuroimaging. - -2) **Annotation and provenance:** Annotating data using standard, reproducible procedures ensures clarity and transparency in data management (*data and metadata management*). **Provenance** refers to the origin and history of data and processes, enabling researchers to track how data was generated, modified, and analyzed (*data and metadata management*, *software management*, and *publishing everything*). This is essential for understanding the context of data and ensuring reproducibility. - -3) **Implementing version control:** Version control is crucial for both data and software management. It allows researchers to track changes over time, revert to previous versions if necessary, and collaborate effectively. - - For data, version control helps manage different versions of datasets and track modifications made during processing and analysis (*data and metadata management*). - - For software, version control helps track code changes, manage different versions of analysis scripts, and ensure that the correct version of the code is used for each analysis (*software management*). - - And even publications can be versioned (*publishing everything*). - -4) **Use of Containers:** Containers provide a portable and self-contained environment for running software, ensuring that the analysis can be executed consistently across different computing environments (*software management*). They encapsulate all the software dependencies needed to run an analysis, making it easier to share software (*publishing everything*) and reproduce results. + + + +1. Study planning + + 1. Implement good science basics (power analysis, statistical consults, etc). + + 2. Use pre-existing data for planning and/or analysis. + + 3. Create an [NIH-compliant data management and sharing plan](https://sharing.nih.gov/data-management-and-sharing-policy/planning-and-budgeting-for-data-management-and-sharing/writing-a-data-management-and-sharing-plan#after). + + 4. Adopt [open consent](https://open-brain-consent.readthedocs.io/en/stable/) to allow broad sharing of data. + + 5. [Pre-register](https://www.cos.io/initiatives/prereg) your study. + + +2. Data and metadata management + + 1. Use standard data formats and extend them to meet your needs. + + 2. Use version control from start to finish. + + 3. Annotate data using standard, reproducible procedures. + + +3. Software management + + 1. Use released versions of open source software. + + 2. Use version control from start to finish. + + 3. Automate the installation of your code and its dependencies. + + 4. Automate the execution of your data analysis. + + 5. Annotate your code and workflows using standard, reproducible procedures. + + 6. Use containers where reasonable. + + +4. Publishing everything (publishing re-executable publications) + + 1. Share plans (pre-registration). + + 2. Share software. + + 3. Share data. + + 4. Make all research objects FAIR. + +## ReproNim's four core actions + +As indicated by the blue highlights in the figure below, four core actions are key to implementing the above principles. + +1. Use of standards. + + Using standard data formats and extending them to meet specific research needs is important for data and metadata management (Principle 2) in reproducible neuroimaging. + +2. Annotation and provenance. + + Annotating data using standard, reproducible procedures ensures clarity and transparency in data management (Principle 2). _Provenance_ refers to the origin and history of data and processes, enabling researchers to track how data was generated, modified, and analyzed (Principles 2, 3, and 4). This is essential for understanding the context of data and ensuring reproducibility. + +3. Implementation of version control. + + Version control is crucial for both data and software management. It allows researchers to track changes over time, revert to previous versions if necessary, and collaborate effectively. + + For data, version control helps manage different versions of datasets and track modifications made during processing and analysis (Principle 2). + + For software, version control helps track code changes, manage different versions of analysis scripts, and ensure that the correct version of the code is used for each analysis (Principle 3). + + And even publications can be versioned (Principle 4). + +4. Use of containers. + + Containers provide a portable and self-contained environment for running software, ensuring that the analysis can be executed consistently across different computing environments (Principle 3). Containers encapsulate all of the software dependencies needed to run an analysis, making it easier to share software (Principle 4) and reproduce results. ![image](/images/principles-of-neuroimaging.jpg) diff --git a/content/resources/tutorials/data-dictionary.md b/content/resources/tutorials/data-dictionary.md index cde4c84..e2a9778 100644 --- a/content/resources/tutorials/data-dictionary.md +++ b/content/resources/tutorials/data-dictionary.md @@ -8,7 +8,7 @@ weight: 5 **[Reproducible neuroimaging principles](/about/in-practice/#repronims-principles-of-reproducible-neuroimaging)** - 2b. Data and Metadata management: Use standard data formats and extend them for your needs -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** - Standards - Annotation diff --git a/content/resources/tutorials/dicom-to-bids.md b/content/resources/tutorials/dicom-to-bids.md index 4c863d3..f81a33d 100644 --- a/content/resources/tutorials/dicom-to-bids.md +++ b/content/resources/tutorials/dicom-to-bids.md @@ -9,7 +9,7 @@ weight: 5 - 2a. Data and Metadata management: Use standard data formats and extend them for your needs -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** - Standards - Annotation diff --git a/content/resources/tutorials/git.md b/content/resources/tutorials/git.md index 7e0128e..dfd8f1f 100644 --- a/content/resources/tutorials/git.md +++ b/content/resources/tutorials/git.md @@ -9,7 +9,7 @@ weight: 5 - 3b: Software management: Use version control from start to finish -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** - Implementing version control diff --git a/content/resources/tutorials/nipoppy.md b/content/resources/tutorials/nipoppy.md index 1d476c1..1b9d475 100644 --- a/content/resources/tutorials/nipoppy.md +++ b/content/resources/tutorials/nipoppy.md @@ -7,7 +7,7 @@ weight: 5 **[Reproducible neuroimaging principles](/about/in-practice/#repronims-principles-of-reproducible-neuroimaging)** -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** **Standards** diff --git a/content/resources/tutorials/pond-lake.md b/content/resources/tutorials/pond-lake.md index 1028d7c..3972809 100644 --- a/content/resources/tutorials/pond-lake.md +++ b/content/resources/tutorials/pond-lake.md @@ -10,7 +10,7 @@ weight: 5 - 1b Study Planning: Consider using pre-existing data for planning or analysis - 2c Metadata management: Annotate your data using standard formats -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** - Use of Standards - Annotation and provenance diff --git a/content/resources/tutorials/publish-everything.md b/content/resources/tutorials/publish-everything.md index 5eaa236..98dacad 100644 --- a/content/resources/tutorials/publish-everything.md +++ b/content/resources/tutorials/publish-everything.md @@ -7,7 +7,7 @@ weight: 5 **[Reproducible neuroimaging principles](/about/in-practice/#repronims-principles-of-reproducible-neuroimaging)** -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** **Standards** diff --git a/content/resources/tutorials/repronim-containers.md b/content/resources/tutorials/repronim-containers.md index 5973017..ec3f29a 100644 --- a/content/resources/tutorials/repronim-containers.md +++ b/content/resources/tutorials/repronim-containers.md @@ -16,7 +16,7 @@ weight: 5 - 3e: **Annotate** your code and workflows using standard, reproducible procedures - 3f: Use **containers** where reasonable -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** - Standards - Annotation diff --git a/content/resources/tutorials/reproschema.md b/content/resources/tutorials/reproschema.md index 25aeb03..7822685 100644 --- a/content/resources/tutorials/reproschema.md +++ b/content/resources/tutorials/reproschema.md @@ -8,7 +8,7 @@ weight: 5 **[Reproducible neuroimaging principles](/about/in-practice/#repronims-principles-of-reproducible-neuroimaging)** - Principle 2c: Data and Metadata management: Annotate data using standard, reproducible procedures -**[Actions](/about/in-practice/#repronims-4-core-actions)** +**[Actions](/about/in-practice/#repronims-four-core-actions)** - Standards - Annotation From 3b1ba2eca7d0e4763bd98ec3883c46800e78650b Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 31 Dec 2024 12:37:46 -0500 Subject: [PATCH 10/10] Edit and style approach page --- content/about/repronim-approach.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/content/about/repronim-approach.md b/content/about/repronim-approach.md index 8c10a67..f3b4587 100644 --- a/content/about/repronim-approach.md +++ b/content/about/repronim-approach.md @@ -6,18 +6,18 @@ weight: 90 ## How does ReproNim help support reproducible neuroimaging? -[ReproNim](https://www.repronim.org/)’s goal is to improve the reproducibility of neuroimaging science, while making the process of capturing and precisely describing all essential/necessary experimental details both easier and more efficient for investigators. +ReproNim's goal is to improve the reproducibility of neuroimaging science while making the process of capturing and precisely describing all essential study details both easier and more efficient. ReproNim focuses on practices and tools that support researchers and software engineers in integrating reproducible principles and actions into their own neuroimaging workflow. -We call this operational framework for reproducible analysis the ReproSystem. ![image](/images/reprosystem.png) -As outlined in the accompanying figure, the ReproSystem framework takes the full experimental cycle of neuroimaging data acquisition, analyses, and publication into account. -This system explicitly includes both data (any of various types, such as scanner acquisition, data converted to BIDS, behavioral data, output of prior analysis) entering into an analysis, and the metadata+provenance (i.e. software versions and computer operating system versions used, processing script, subject demographics, results description, etc.) of the analysis. -The metadata maintains a link to its associated data permitting flexibility regarding how each of these types of information sources can be used. -To the familiar components of data and analysis environments, we also add to the framework a means to store and retrieve machine-readable description of metadata associated with the tools in both a local/private store (which we refer to as a ReproPond) and a shared/public repository (ReproLake). +As outlined this figure, ReproNim's system takes the full cycle of neuroimaging data acquisition, analyses, and publication into account. +The system explicitly includes both data entering into an analysis (data of various types including scanner acquisitions, data converted to BIDS, behavioral data, and outputs of prior analyses), and the metadata and provenance of the analysis (software versions and computer operating system versions used, processing scripts, subject demographics, results descriptions, etc.). +The metadata maintains a link to its associated data, permitting flexibility in how each of these information sources can be used. +To the familiar components of data and analysis environments we also add a means to store and retrieve machine-readable descriptions of metadata associated with the tools in both a local/private store (which we refer to as a _ReproPond_) and a shared/public repository (_ReproLake_). To get started, see: * [Getting started with ReproNim](/resources/getting-started/) -* The ReproGuide to [tools and use cases](/resources/tools/) +* [ReproNim's core tools](/resources/tools/) +* [ReproNim's tutorials](/resources/tutorials/)