This Open Letter is the outcome of the Sept 2016 conference at Janelia Research Campus on Collaborative Development of Data-Driven Models of Neural Systems. The signatories of the letter commit to making important parts of their research output open source and will require the same level of openness in work they are asked to review.
This initiative has been described in a recent NeuroView article in Neuron: A Commitment to Open Source in Neuroscience, Gleeson et al. 2017.
Dear colleagues,
Neuroscientists are increasingly relying on custom built software to help analyze their experimental data and to construct and run models. Packages for extracting, translating, analyzing and visualising data, as well as scripts for modelling and simulating the mechanisms underlying the examined phenomena, are an essential part of the work behind many publications in the field today. These scripts can often be complex and involve many processing steps which can’t be fully described in the accompanying publications. Making these publicly available would increase the reproducibility and scientific rigour of the results described. At present though, releasing these is generally not a prerequisite for publication.
A distributed, open and freely available network of tools, databases, and related resources for data analysis and model development will also facilitate reuse of code, making neuroscience research more flexible, efficient and reliable. Ensuring the public availability of all computational models and analysis tools used in publications is crucial for establishing and maintaining such a global infrastructure.
Towards that end, we pledge to release promptly, completely, and freely all computer code, model scripts, and parameters necessary to reproduce the analyses and simulations from any of our new publications. We will make all software applications (tools, libraries, etc.) we develop for experimental data analysis or model construction open source at time of publication, whether or not the application is the main subject of the paper. Furthermore, if and when asked to serve as peer-reviewers, we will henceforth ask authors about the availability of any code they have developed for data analysis and modelling which is essential to reproducing the results of their paper and require that this be shared publicly upon acceptance. We invite all like-minded scientists, developers, users, and peers to join us in this pledge.
- Giorgio A. Ascoli (George Mason University, Fairfax, VA, USA)
- Andrew P. Davison (CNRS, Gif-sur-Yvette, France)
- Padraig Gleeson (University College, London, UK)
- R. Angus Silver (University College, London, UK)
- Kim T. Blackwell (George Mason University, Fairfax, VA, United States)
- Sharon Crook (Arizona State University, United States)
- Ivan Soltesz (Stanford University, United States)
- Salvador Dura-Bernal (SUNY Downstate, United States)
- Malin Sandström (INCF, Sweden)
- Zbigniew Jędrzejewski-Szmek (George Mason University, Fairfax, VA, United States)
- Hanchuan Peng (Alen Institute for Brain Science, United States)
- Matteo Cantarelli (OpenWorm Foundation, United Kingdom)
- Boris Marin (Independent Researcher, Brazil)
- Rick Gerkin (Arizona State University, United States)
- Anton Arkhipov (Allen Institute for Brain Science, United States)
- Szabolcs Káli (Institute of Experimental Medicine, Hungarian Academy of Sciences,Hungary)
- David J. Hamilton (George Mason University, Fairfax, VA, United States)
- Alexander O. Komendantov (George Mason University, Fairfax, VA, United States)
- Keivan Moradi (George Mason University, Fairfax, VA, United States)
- Nelson Spruston (HHMI Janelia Research Campus, VA, United States)
- Sridevi Polavaram (George Mason University, Fairfax, VA, United States)
- Christopher L. Rees (George Mason University, Fairfax, VA, United States)
- Diek W. Wheeler (George Mason University, Fairfax, VA, United States)
- Dean Buonomano (UCLA, United States)
- William Lytton (SUNY Downstate, United States)
- Joe W. Graham (SUNY Downstate, United States)
- Jason Sherfey (Boston University, United States)
- Sam Neymotin (Brown University, United States)
- Mario Negrello (Erasmus MC, Netherlands)
- Michele Migliore (Institute of Biophysics, National Research Council, Palermo, Italy)
- David Kleinfeld (University of California at San Diego, United States)
- Sergio Solinas (University of Sassari, Sardinia, Italy)
- Erik De Schutter (Okinawa Institute of Science and Technology, Japan)
- Shreejoy Tripathy (University of British Columbia, Canada)
- Alain Destexhe (CNRS, Gif sur Yvette, France)
- Dimitri Kullmann (University College London, United Kingdom)
- Georg Keller (Friedrich Miescher Institute, Basel, Switzerland)
- Zoltan Nusser (Inst. of Experimental Medicine, Budapest, Hungary)
- Peter Latham (UCL, United Kingdom)
- Rosa Cossart (INMED, INSERM U901, Aix-Marseille University, France)
- Andrew MacAskill (University College London, United Kingdom)
- Nicholas Lesica (University College London, United Kingdom)
- Nathalie Rochefort (University of Edinburgh, United Kingdom)
- Horacio G. Rotstein (New Jersey Institute of Technology, United States)
- Javier DeFelipe (Instituto Cajal (CSIC) and Laboratorio Cajal de Circuitos Corticales (CTB/UPM), Spain)
- Pedro Garcia-Rodriguez (CNRS, France)
- Daniel Bush (UCL Institute of Cognitive Neuroscience, United Kingdom)
- Tiago Branco (UCL Sainsbury Wellcome Centre, United Kingdom)
- Stefan Remy (German Center for Neurodegenerative Diseases, Bonn, Germany)
- Attila Losonczy (Columbia University, United States)
- Andreas Schaefer (The Francis Crick Institute and University College London, United Kingdom)
- Fritjof Helmchen (University of Zurich, Switzerland)
- Frances Skinner (Krembil Research Institute, University Health Network and University of Toronto, Canada)
- Stephen J Eglen (University of Cambridge, United Kingdom)
- Henry Markram (Blue Brain Project, Switzerland)
- Jean-Denis Courcol (Blue Brain Project, Switzerland)
- Hanchuan Peng (Allen Institute for Brain Science, United States)
- Ze Wang (Temple University, United States)
- Xiaoliang Zhao (Mayo Clinic, United States)
- Ting Zhao (Janelia Research Campus, United States)
- Ziqiang Wei (Janelia Research Campus, United States)
- Weidong Cai (The University of Sydney, Australia)
- Tadashi Yamazaki (The University of Electro-Communications, Japan)
- Kevin Allen (University of Heidelberg, Germany)
- Jiannis Taxidis (UCLA, United States)
- Han Kyoung Choe (DGIST, Korea)
- Dan Goodman (Imperial College London , United Kingdom)
- Majid Mohajerani (University of Lethbridge, Canada)
- Andre Marques-Smith (UCL, United Kingdom)
- Sarang Dalal (Aarhus University, Denmark)
- Rob Brownstone (University College London, United Kingdom)
- Jake Harland (KCL student, United Kingdom)
- Henry Lütcke (ETH Zurich, Switzerland)
- Angus McMorland (University of Auckland, New Zealand)
- Remigijus Lape (University College London, United Kingdom)
- Lucia Sivilotti (UCL, United Kingdom)
- Zé Henrique Targino (Brain Institute, UFRN, Brazil)
- Fleur Zeldenrust (Radboud University / Donders Institute, Netherlands the)
- Jonathan Vacher (Albert Einstein College of Medicine, United States)
- Mark D Humphries (University of Manchester, United Kingdom)
- Renato Duarte (Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (JBI-1 /INM-10), Jülich Research Centre, Jülich, Germany, Germany)
- Barna Zajzon (Institute of Neuroscience and Medicine (INM-6), Jülich Research Center, Germany)
- Subutai Ahmad (Numenta, United States)
- Laurent Perrinet (Institut de Neurosciences de la Timone, France, French Republic)
- Pierre Yger (Institut de la Vision, INSERM, France, French Republic)
- Justin Kiggins (Allen Institute for Brain Science, United States)
- Lekhnath Sharma Pathak (Tribhuvan University, Nepal)
- Niamh M. C. Connolly (Royal College of Surgeons in Ireland, Ireland)
- Mathew H Evans (University of Manchester, United Kingdom)
- Marcel Stimberg (Institut de la Vision, UPMC, Paris, France, French Republic)
- Arthur Leblois (CNRS, France, French Republic)
- Tom Tetzlaff (Jülich Research Center, Germany)
- Jakob Kisbye Dreyer (University of Copenhagen, Denmark)
- Stefan Hallermann (University of Leipzig, Germany)
- Martha S Burns (Northwestern University, United States)
- Randy McIntosh (Rotman Research Inst - Baycrest, Univ of Toronto, Canada)
- Sophie Lambert (Allen Institute for Brain Science, United States)
- Luke Campagnola (Allen Institute for Brain Science, United States)
- Peter Groblewski (Allen Institute for Brain Science, United States)
- Matthew Valley (Allen Institute for Brain Science, United States)
- xiaoxuan jia (Allen Institute, United States)
- Josh Siegle (Allen Institute, United States)
- Yazan N. Billeh (Allen Institute for Brain Science, United States)
- Rui Liu (Allen Institute for Brain Science, United States)
- Anatoly Buchin (ALLEN INSTITUTE FOR BRAIN SCIENCE, United States)
- Corinne Teeter (Allen Institute for Brain Science, United States)
- Bradley Voytek (UC San Diego, United States)
- Michael Baylor (Computational Neuroscientist, United States)
- Harsh Sikka (Harvard University, United States)
- Thomas Donoghue (UC San Diego, United States)
- Jennifer D. Whitesell (Allen Institute for Brain Science, United States)
- Jun Zhuang (Allen Institute for Brain Science, United States)
- Rylan S Larsen (Allen Institute For Brain Science, United States)
- Amy Bernard (Allen Institute for Brain Science, United States)
- Pierre Le Merre (Karolinska Institutet, Sweden)
- Siva Venkadesh (George Mason University, United States)
- Justas Birgiolas (Arizona State University, United States)
- Antje Märtin (Karolinska Institutet, Sweden)
- Cantin Ortiz (Karolinska Institutet, Sweden)
- Nicolas Giret (CNRS, Université Paris Sud, Orsay, France, French Republic)
- Ying Wang (Donders Institute, Radboud University, Netherlands the)
- Nicolas Guyon (Karolinska Institutet, Sweden)
- Robert Oostenveld (Donders Institute, Radboud University, Netherlands the)
- Kristijan Armeni (Donders Institute, Radboud University, Netherlands the)
- Bradly Alicea (OpenWorm Foundation, United States)
- Antoine Chaillet (CentraleSupélec, Univ. Paris Saclay, IUF, France, French Republic)
- Nicolas P. Rougier (Inria, France, French Republic)
- Shailesh Appukuttan (UNIC, CNRS, France, French Republic)
- Gergo Orban (MTA Wigner RCP, Hungary)
- Nawal El Boghdady (UMCG, Netherlands the)
- Daniel K Wójcik (Nencki Institute of Experimental Biology, Poland)
- Alex Cope (University of Sheffield, United Kingdom)
- Michael Schmuker (University of Hertfordshire, United Kingdom)
- Hans Brünner (Karolinska Institute, Sweden)
- David Golomb (Ben-Gurion University, Israel)
- Christoph Metzner (University of Hertfordshire , United Kingdom)
- Vladislav Sekulic (Uppsala University, Sweden)
- Tjeerd Boonstra (University of New South Wales, Australia)
- Arne F Meyer (University College London, United Kingdom)
- Luc Berthouze (University of Sussex, United Kingdom)
- Torbjørn V Ness (Norwegian University of Life Sciences, Norway)
- Johannes Niediek (University of Bonn, Germany)
- Dominique Makowski (Université Sorbonne Paris Cité, France, French Republic)
- Eric S. Kuebler (University of Ottawa, Canada)
- Antonio Roque (Universidade de São Paulo, Brazil)
- Jérémy Fix (CentraleSupelec , France, French Republic)
- Yoelis Acourt (Cobaye, France, French Republic)
- Jan Funke (UPC Barcelona, Spain)
- Andre Fabio Kohn (University of Sao Paulo, Brazil)
- Ankur Sinha (UH Biocomputation, University of Hertfordshire, UK, United Kingdom)
- Alessandro Tavano (Max Planck Institute for Empirical Aesthetics, Frankfurt, Germany)
- Johannes Hjorth (KTH, Royal Institute of Technology, Sweden)
- Peter Andras (Keele University, United Kingdom)
- Alejandro Tabas (Max Planck Institute for Brain and Human Cognitive Sciences, Germany)
- Johanni Brea (EPFL, Switzerland)
- Klaus Wimmer (CRM Barcelona, Spain)
- Alexander Kozlov (KTH - Royal Institute of Technology, Sweden)
- Osame Kinouchi (Universidade de São Paulo, Brazil)
- Eleni Vasilaki (University of Sheffield, United Kingdom)
- Simon M. Danner (Drexel University College of Medicine, United States)
- Artur Luczak (Univ of Lethbridge, Canada)
- Silvia Maggi (University of Manchester, United Kingdom)
- Alberto Antonietti (Politecnico di Milano, Italy)
- Sylvain Baillet (McGill University, Canada)
- Gaël Varoquaux (Inria, France, French Republic)
- Volker Steuber (University of Hertfordshire, United Kingdom)
- Shabnam Hakimi (Duke University, United States)
- Gaute Einevoll (Norwegian University of Life Sciences & UiO, Norway)
- Alessio Buccino (University of Oslo, Norway)
- Koen Vervaeke (University of Oslo, Norway)
- Tuomo Mäki-Marttunen (Simula Research Laboratory, Norway)
- Kristy Ly (CSU Fresno, United States)
- Renaud B. Jolivet (University of Geneva and CERN, Switzerland)
- Dominik Krzeminski (Cardiff University, United Kingdom)
- Kayson Fakhar (Carl von Ossietzky University of Oldenburg, Germany)
- Balazs B Ujfalussy (Inst. of Experimental Medicine, Budapest, Hungary)
- Tiago Azevedo (University of Cambridge, United Kingdom)
- Torkel Hafting (University of Oslo, Norway)
- Jeremy Guillon (ARAMIS LAB, Brain and Spine Institute, France, French Republic)
- Hans Ekkehard Plesser (Norwegian University of Life Sciences, Norway)
- Maryann Martone (UCSD, United States)
- Mikkel Elle Lepperød (University of Oslo, Norway, Norway)
- Bruce Graham (University of Stirling, United Kingdom)
- Pierre Berthet (University of Oslo, Norway)
- Kerstin Lenk (TU Dresden, Germany)
- Abolfazl Ziaeemehr (Institute of advanced studies on basic science, Iran)
- Austin Soplata (Boston University, United States)
- Esin Karahan (Cardiff University Brain Research Imaging Centre, United Kingdom)
- Johannes Fahrenfort (University of Amsterdam / Vrije Universiteit Amsterdam, Netherlands the)
- Milad H. Mobarhan (University of Oslo, Norway)
- Won Chan Oh (KIST (Korea Institute of Science and Technology), Korea)
- Rui Ponte Costa (University of Oxford, United Kingdom)
- Ted Carnevale (Neuroscience Department, Yale University, United States)
- Alexandre HYAFIL (Universitat Pompeu Fabra, Spain)
- Andrea Insabato (University Pompeu Fabra, Spain)
- Andrea Pisauro (University of Glasgow, United Kingdom)
- Jesus Bas (UPF, Spain)
- Janelle Pakan (Otto von Guericke University, Germany)
- Kiro Stojanoski (Institute of Chemistry, Faculty of Science, Sts. Cyril and Methodius University, Skopje) (Professor, Macedonia)
- Eric Maris (Donders Institute for Brain, Cognition and Behaviour, Netherlands the)
- Gregory J Gage (Backyard Brains, United States)
- Hamza AlGhamdi (King Faisal Medical City, Saudi Arabia)
- Zahid I. (University of Toronto CPIN, Canada)
- Chun Yao (McGill University, Canada)
- Yaneri A. Ayala (Instituto de Neurobiología, UNAM., Mexico)
- Matheus Cafalchio de Oliveira (PhD, Ireland)
- Y. H. Chan (Nanyang Technological University, Singapore)
- Sabitha Rani B.S (CUSAT, India)
- Rajan Kashyap (National University of Singapore, Singapore)
- Upinder S. Bhalla (NCBS/TIFR, India)
- chaochun chuang (National center for high-performance computing, Taiwan)
- Fabrizio Parente (La Sapienza, Italy)
- Rembrandt Bakker (Radboud University Nijmegen, Netherlands the)
- Adriana Braescu (Re-Design ngo, Romania)
- Lesa Hollen (Independent Neuroscientist, United States)
- Angie Laird (Florida International University, United States)
- Ali Arshad (Dawson College, Canada)
- mohamadreza (Graduate Student of Biomedical, Isfahan University of Medical Science, Iran)
- Jeffrey S. Grethe (University of California, San Diego, United States)
- Bianca Condorachi (Dawson College, Canada)
- Matthew Brett (University of Birmingham, United Kingdom)
- Florian Ph.S Fischmeister (University of Graz, Austria)
- Emanuele Olivetti (Bruno Kessler Foundation, Italy)
- Alexandre Gramfort (INRIA, France, French Republic)
- Thomas Pengo (University of Minnesota, United States)
- Sajid Bashir (PINUM Cancer hospital, Pakistan)
- Pankaj Gupta (University of British Columbia, Canada)
- Al Fermelia (CLM Associates, United States)
- Xiaolu Qiu (University of Louisville, United States)
- Satrajit S Ghosh (MIT/HMS, United States)
- Philippe Poulin (Université de Sherbrooke, Canada)
- Md Nurul Islam (Trinity College Institute of Neuroscience, Ireland)
- Claudia Clopath (Imperial College London, United Kingdom)
- Masoud Nosratabadi (University of social welfare and rehabilitation, Iran)
- Norman Kong (Dawson College, Canada)
- Svenn-Arne Dragly (University of Oslo, Norway)
- Flavio Mourao (Universidade Federal de Minas Gerais, Brazil)
- Miguel Xochicale (University of Birmingham, United Kingdom)
- Gilles Courtand (Institut de Neurosciences Cognitives et Intégratives d’Aquitaine - cnrs, France, French Republic)
- Zailyn Tamayo (Yale University, United States)
- Claus Volko (Independent Scholar, Austria)
- Sean Martin (Trinity College Institute of Neuroscience, Ireland)
- Itamar F. Lima (Faculdade Estácio de Alagoas, Brazil)
- Vikas Singh (VA Medical Center, United States)
- Yukti Chopra (Indian Institute of Science, India)
- Guang-Wei Zhang (University of Southern California, United States)
- Erick Olivares (University of Texas at San antonio, United States)
- Vsevolods Girsovics (Institute of Pathophysiology, Germany)
- Sebastian Sprerizer (Research center Jülich, Germany)
- Michele Giugliano (SISSA, Italy)
- Soumya (Manipal Institute of Technology, India)
- M. Anil Tuncel (Blue Brain Project, Switzerland)
- Aaradhya Vaze (Indian Institute of Science Education and Research, India)
- Patrick (De Montfort University, United Kingdom)
- You-Yin Chen (National Yang Ming University, Taiwan)
- María E. Castelló (Instituto de Investigaciones Biológicas Clemente Estable (MEC), Uruguay)
- Hidenori Aizawa (Hiroshima University, Japan)
- Cooper Smout (Queensland Brain Institute, Australia)
- Bryce Dunn (George Mason University, United States)
- Sina Mansour L. (The University of Melbourne, Australia)
- Christian Eduardo Méndez Coronel (Instituto Nacional de Psiquiatría Ramón de la Fuente Múñiz, Mexico)
- Dylan Gomes (NRC postdoc (NOAA Fisheries), United States)
- Fatih Celik (Ege University, Turkey)
- Avishek (Interdisciplinary Institute for Neuroscience, France, French Republic)
- Alexander Socop (National Taiwan Normal University, Taiwan)
- Yoshihiro Okumura (RIKEN, Japan)
- Elliott Trives (INRAE, France, French Republic)
- Danish A. Shahid (Pakistan Army Medical Corps, Pakistan)
- Wan Mohd Ridzwan Ramlee (Institute, Malaysia)
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Frequently Asked Questions
What type of scripts will be expected for a typical experimental paper?
It would be good to release the key scripts for transforming raw experimental data into the figures used to present/interpret results. At least one of the panels of the figures in the paper should be reproducible from the scripts, ideally more. For analysis of experimental data this will often mean that some of the raw data or partially analyzed results will need to be included, so that the scripts can be successfully run on another machine. Journal requirements for data availability are currently stricter than for code and many journals already require data availability statements from authors. Distributing the relevant subset of data with the figure (e.g. in the same GitHub repository) would greatly facilitate use of the scripts.
Note that scripts should not need to produce the final (formatted) figures themselves, just the relevant traces/graphs to demonstrate that the analysis pipeline can be locally reproduced.
What about analysis of experimental data which requires proprietary/commercial software to run?
Many commercial applications for acquiring and processing experimental data use proprietary formats and it can often be difficult or impossible to reproduce such analyses without access to these applications. There is not a requirement that code released by labs should be executable on freely available software, but it would be ideal if files were released which would make it possible to reproduce the analysis steps by someone with access to the same version of the application used.
A key reason to make these scripts available is the transparency which comes from having access to the algorithms/parameters used in the code, which may not be outlined in full in the paper. Releasing scripts in MATLAB or IgorPro for example would allow someone to see the processing steps without the need to run the scripts in the original application.
Some proprietary applications allow export of files in their native formats to more open (or graphical) formats and making these available (in addition to the proprietary files) is encouraged.
What about custom code developed to drive hardware?
Labs regularly need to develop code to run and manage (custom) hardware for acquiring data. This type of code is not covered by this pledge, as such software would be highly dependent on the hardware involved and would not necessarily advance the scientific interpretation of the results. The point at which acquired data is saved (“raw” experimental data) and custom scripts are used to further process it, is the point at which this pledge applies. Nevertheless, developers of such code for controlling hardware could well benefit from releasing it (in terms of encouraging reuse/testing, code/bugfix contributions) if the hardware is widely used in the field.
Will this apply to all previous publications by labs which sign this pledge?
No. This commitment to produce analysis scripts only covers papers published after the letter has been signed. However, if labs reuse and further develop code and models between publications/projects, releasing the code openly can lead to better reproducibility of their past publications also.
Will the labs which release code be obliged to maintain the code?
No. There is no implied suggestion that the scripts are useful for any other purpose than reproducing the results of the referenced publication. While someone should be able to get the scripts running on their own machine and produce a figure from the relevant paper, there is no requirement that the scripts should be generic or structured/commented sufficiently that they can be repurposed for use with other data, unless, of course, the publication is specifically about a general purpose analysis pipeline. If someone has trouble running the scripts for the stated purpose, they can reasonably get in contact with the authors for clarification, but they should not expect support for modifying them for other purposes.
Note however that the lab releasing the scripts can certainly claim that they are general purpose and can potentially get bug fixes/tips/extensions from others trying out the code. The README accompanying the scripts should make it clear about the general usefulness of the code and whether such contributions are encouraged.
Won’t extra time/funding be required to get the code into a releasable form?
It shouldn’t. If the scripts are well written enough to be confidently used for generating the results presented in the paper, they should be sufficiently well written to be released. The step of assembling a consistent/minimal/stable set of scripts from the various versions used during the paper writing process is an important quality control step, and should not be seen as additional work.
Does this apply to all software developed in labs which sign the pledge?
No. Labs can be involved in multiple projects, some unpublished, some commercial, and not all code being developed is appropriate for release under an open source licence. This pledge only covers scripts for data analysis and computational models which are related to published works, and which are essential to reproducing the data processing and modelling/simulation stages of those scientific results.
What licences should be used?
There is no stipulation on what types of open source licence should be used for the scripts, but it is highly recommended to include details of a licence when distributing the code. See choosealicense.com which discusses the various options related to open source software.
Note that funding agencies increasingly have detailed requirements on licensing of publications funded by them (e.g. Wellcome Trust now specifies CC-BY for publications) and specific requirements on the licences for sharing of data and code will not be far behind. Checking the latest details with your with funding agency is advised.
Where should scripts be deposited?
There are many user friendly, free code sharing websites available for hosting open source software, including GitHub and BitBucket. ModelDB is a well established archive for sharing models in computational neuroscience. Open Source Brain is a resource specifically designed to allow collaborative development of models in neuroscience, and links to the source code on public repositories like Github. Figshare provides a location to share large volumes experimental data, and associated scripts can be placed here too, if they are unlikely to change much over time. More information on this can be found here.
Aren’t the journals’ own data/code sharing requirements sufficient to ensure these scripts should be made available?
While an increasing number of journals actively encourage authors to make these types of scripts available, few make publication dependent on providing them. Many journals will now require a data availability statement which should state whether these scripts are available. See Nature's discussion on this.
Will the signatories be required to reject manuscripts/grants they review which do not make any code available?
This should be on a case by case basis and will depend on the judgement of the reviewer about how essential the scripts are to the key results discussed in the manuscripts. It will ultimately be up to the editors to decide whether such requests are reasonable.
The desired effect is of this pledge is that researchers will be aware that there are a body of potential reviewers out there who will ask about code availability. Planning to ultimately release code related to manuscripts or making specific commitments to open source in grant proposals will help avoid problems at a later stage.
If we are collaborating with a lab not signing this pledge, should we feel bounded by this commitment?
This should be dealt with on a case-by-case basis. As a general rule of thumb, if you are the corresponding author and/or you’re a main developer of the scripts, it is reasonable to insist on the associated scripts being available/open; if your role on the paper is minor and not related to the scripts, then actively encouraging your fellow authors in this direction is advised.