Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy
Cancer Research 2019; 79:6227–6237
Compute Capsule: RadioGx: Modeling cellular response in large-scale radiogenomic databases to advance precision radiotherapy
The Reproducibility Project: Cancer Biology has clearly highlighted the need for published articles to contain more detail of exactly how each study was conducted. This page describes AACR journal efforts and useful resources to assist authors with improving the reproducibility of their published research article.
Article length requirements should not constrain authors in the reporting of critical methodological details, nor should important methods information be relegated to the supplementary materials. As part of the ongoing efforts of the AACR journals to improve the reproducibility of the research they publish, the “Materials and Methods” or “Methods” section in original research articles is no longer included when calculating the length of a submitted article. Moreover, the journals will actively screen for manuscripts that appear to have overly short descriptions of the methods and will ask authors to expand them as necessary.
Authors are requested to make use of the resources below wherever relevant to provide further transparency to their submitted study and thereby improve the reproducibility of the work.
Study Rigor and Reporting
This automated tool screens methods text for adherence to experimental rigor and reporting requirements and provides the author, editors, and reviewers with a standardized report and overall score for their submission. Authors are encouraged to consult the report and revise their manuscript as appropriate to improve reporting.
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Study Resource IDs
Authors are asked to include unique searchable IDs called Research Resource Identifiers (RRIDs) in their manuscript to uniquely identify the antibodies, experimental models, recombinant DNA, and software used in their study. This resource provides critical unambiguous methodological information for readers.
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Study Code and Data
For studies relying on custom software code for data analysis, authors are strongly encouraged to use this free cloud-based computing environment to provide reviewers and readers with seamless browser-based access to the code and data behind their manuscript. This resource allows others to easily reproduce and build on the analyses.
Learn more »
Authors are encouraged to publish the step-by-step protocol(s) used in their study at protocols.io and then include the unique digital object identifier(s) (DOI) in the methods section of their research article.
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Cell Line Authentication
AACR authors must document the authentication of all cell lines used in their study. The resources below are provided to assist authors with this requirement.
Information and Guidelines
Guide to Human Cell Line Authentication from the International Cell Line Authentication Committee (ICLAC)
Register of Misidentified Cell Lines maintained by ICLAC
Cell Line Authentication Test Recommendations from ATCC, with important guidance on cell passaging
UKCCCR Guidelines for the Use of Cell Lines in Cancer Research
Cell Line Authentication Service Providers*
- ATCC - NA
- BioReliance (MilliporeSigma) - WW
- Bio-Synthesis - NA
- CellBank Australia - AU
- Cell Line Genetics - NA
- Charles River - WW
- Creative Bioarray - NA
- DNA Forensics Laboratory - IN
- ECACC - EU
*Not endorsed by AACR. NA=North America, WW=World Wide, and EU= Europe. Other abbreviations are standard country codes.
This automated methods-review tool screens submitted manuscript text for adherence to experimental rigor and reporting requirements.
To assist authors in improving the reproducibility of submitted manuscripts, the AACR journals have integrated our manuscript submission system, SmartSubmit, with SciScore.
SciScore scans the methods section of an author’s submitted manuscript and uses machine learning methods to check for multiple indicators of experimental rigor and proper reporting of the resources used. The tool then provides the author with a report containing easy-to-use tables on rigor adherence and key resources such as antibodies, experimental models, recombinant DNA, and software. The report clearly communicates what the tool did and did not find, and displays an overall numerical score from 0 to 10, based on the findings.
Importantly, SciScore also checks whether the experiments described in the manuscript used any known misidentified or contaminated cell lines. If any are detected, the SciScore report prominently highlights this.
Authors are strongly encouraged to use the SciScore report to ensure that key information related to reproducibility is included in their manuscript whether they are revising it for submission to an AACR journal or another publisher.
The SciScore report is made available to the journal editors and reviewers but isn’t currently a formal part of their evaluation. Prior to acceptance, authors are asked to use the report’s list of key resources to add RRIDs to their manuscript for all listed resources (see RRID section below). The SciScore report will also be used by journal staff when performing standard manuscript quality checks before acceptance. Authors will be asked to address any outstanding reporting issues.
For more information, including how you can use your ORCID to run the report for free yourself prior to submission, please see the frequently asked questions page on the SciScore site and this sample report.
Author inclusion of unique searchable IDs for the antibodies, experimental models, recombinant DNA, software, and other resources used their manuscript, provides critical unambiguous methodological information for readers.
To uniquely identify the biological reagents and other types of resources reported in the Materials and Methods of published research articles, the AACR asks its authors to include unique searchable Research Resource Identifiers (RRIDs), as assigned by the Resource Identification Initiative. The process of identifying resources in need of RRIDs and assigning the correct RRID is greatly facilitated by the SciScore report described above.
In addition to uniquely identifying each reagent and tool, these RRIDs can be used to link readers to external resources and enable search engines to return all articles in which a resource was used. We believe these are important steps toward ensuring reproducible methods and providing critical data to help researchers identify suitable reagents and tools, and we are now asking authors to include RRIDs in their manuscripts.
How to find an RRID
When submitting a manuscript to the AACR journals, the corresponding author will receive a SciScore report containing a Key Resources Table listing all the reagents and other resources that SciScore detected in the methods section of the manuscript. Beside each resource is a suggested RRID and link to the resource description. Click the link to verify that this is the exact resource used in the described research.
To obtain an RRID for a resource mentioned somewhere other than the methods section of a submitted manuscript, please visit the Resource Identification Portal and enter appropriate search term(s) for the reagent you used. Tips for searching are provided below.
- Antibodies: searching for the catalog number usually narrows the search to only a few relevant results.
- Cell Lines: searching for the catalog number of an established cell line is usually best, searching for common cell lines such as HeLa cells is expected to produce several pages of results. The cell line information page will indicate whether the cell line is one of over 480 misidentified cell lines cataloged in the Register of Misidentified Cell Lines. Please also see our cell line authentication policy.
- Organisms: you may include PubMed IDs (PMIDs) in your search or filter your search results by PMID, species, phenotype, and other criteria.
- Software Tools: usually the name of the tool (MATLAB or ImageJ) or the institution where it is housed will return relevant results.
- Online Resource: usually the name of the online resource.
How to include RRIDs
Once you have located an RRID, please insert "RRID:" plus the identifier in the appropriate location in the Materials and Methods section of the manuscript. For example:
- Antibodies: "Sections were stained with a rabbit polyclonal antibody against ERK1 (Abgent Cat# AP7251E, RRID: AB_2140114)."
- Cell Lines: "Hela cells (CLS Cat# 300384/p699_HeLa_S3, RRID: CVCL_0058) were obtained from...”
- Organisms: "Fgf9Eks/Fgf9+ mice (RRID: MGI_3840442) were fed..."
- Software Tools: "...terminals were mapped with a computer-assisted mapping program (Neurolucida, v 10; MicroBrightField RRID: nif-0000-10294)."
How to request an RRID
If you cannot find an RRID for a resource that you used, please submit the reagent as detailed below so that it can be given proper identifiers for future use. The Resource Identification Portal includes mouse, zebrafish, worm, fruit fly, and rat model organisms as well as many commercial antibodies and some lab-sourced ones. When you cannot find an RRID for one of these five model organisms, please see these instructions for submitting a new organism to the relevant model organism database. Antibodies can be added via the Antibody Registry; please note that a login is required on that site.
This free cloud-based computing environment provides reviewers and readers with seamless browser-based access to the code and data behind manuscripts so that they can reproduce the analyses used by the authors.
Researchers are increasingly relying on algorithms implemented in software to process and analyze their data. Without the computer code and associated test or real data, it is difficult for others to reproduce or reuse the authors’ analysis methods. To help solve this problem, the AACR journals have integrated their submission system, SmartSubmit, with Code Ocean, a free cloud-based service that allows authors to provide the data, code, and computing environments used in their analyses in the form of a Code Ocean “compute capsule.” This capsule will be linked to their manuscript so that editors and reviewers may easily reproduce and examine the exact data analyses performed by the authors. Upon publication, the capsule may be linked to the published manuscript so that the compute capsule is accessible inline in the published article through a widget (see examples below). Readers may then easily reproduce and build on the authors’ work.
During manuscript submission, authors are asked if they wish to provide code associated with the work described in their submission. If they already have a git repository of the pertinent code, it can be imported with the click of a button, cleaned up, validated, and provided to editors, reviewers, and readers. We strongly encourage all authors who used code for any of their data analysis to provide the software code, with either test or actual raw data, in a Code Ocean compute capsule.
We therefore encourage authors to provide their software code, with either test or actual raw data, in a Code Ocean compute capsule so that others to easily run, edit, and reuse the code in a cloud-based computing environment from their web browser.
All authors with a Code Ocean compute capsule associated with a manuscript should include a statement in their manuscript describing the capsule and a link in the form: https://codeocean.com/capsule/XXXXXXX/ (where X is the unique identifier of the capsule).
Examples of published articles from AACR journals with code and data are provided below.
Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy
Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts
Cancer Research 2019; 79:4539–4550
Compute Capsule: Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts
AXL Is a Putative Tumor Suppressor and Dormancy Regulator in Prostate Cancer
Molecular Cancer Research 2019; 17:356–369
Compute Capsule: AXL - putative tumor suppressor and dormancy regulator in prostate cancer
A free platform allows authors to publish clear step-by-step methods protocols that can be directly linked to from their research articles.
It is generally recognized that the traditional Methods section in published research articles has insufficient details for readers to reproduce the results. To help address this, we encourage authors to publish the step-by-step protocol(s) used in their study at protocols.io and then include the unique digital object identifier(s) (DOI) in the Materials and Methods of their research article.
How to publish your Protocol at protocols.io
Protocols.io provides a free platform for researchers to publish their protocols and control who can view them. An available app allows each protocol to be conveniently run in a mobile device at the bench.
- Create a free account at protocols.io.
- Enter the step-by-step details and comments for your protocol and then follow the instructions here: https://www.protocols.io/help/publish-articles.
- Select either ‘Publish’ or ‘Reserve DOI’ to generate the link(s) to put in your manuscript (it is recommended to publish and make fully available but appreciate that some will want their protocol private initially).
How to link to your Protocol from your manuscript
By linking to protocols from within a submitted manuscript, both reviewers and readers will be able to directly access and read the full protocol at protocols.io.
- Provide editor and reviewer access by Including the DOI (and private) link(s) and a reference for your protocol in the methods section of your manuscript using the format provided by protocols.io: http://dx.doi.org/10.17504/protocols.io.xxxxxxx (where xxxxxxx is the unique DOI).
- If the DOI was reserved, you’ll need to return to your protocol and select ‘Publish’ to make the protocol publicly available when your manuscript is accepted. Remember to also remove any private links from your manuscript and only leave the DOI.