Standard Bio-101 Protocol Format
Authors are encouraged (but not required) to follow the standard Bio-101 format for initial submissions. The Bio-101 editing team will do the required formatting for authors to ensure that all protocol submissions follow the standard Bio-101 format. Protocols published at Bio-101 contain the following 12 elements:
- Protocol Title
The title should indicate the goal of the protocol and provide enough details to help prospective researchers determine whether the protocol is of interest to them. Keep in mind that your protocol could be useful for researchers from a completely different field. Ensure that the wording of title can be understood by a broad range of scientists.
- Abstract
The abstract should provide a brief summary of the protocol, highlighting its goals and expected outcomes. It should also describe a context in which the assay/method can be employed.
- Materials and Reagents
Write this section for a reader who is a novice. This section should provide a detailed list of all materials and reagents required for the successful completion of the experiment. Please specify manufacturer catalog numbers for critical materials. We also recommend that authors provide storage temperature and shelf life for important reagents.
- Equipment
The above instructions for materials and reagents also apply for equipment. List specific catalog/model numbers for equipment where appropriate.
- Procedure
Authors are encouraged to list all steps of the procedure chronologically as it makes the protocol much easier to follow. At crucial steps, authors should make sure to include advice from personal experience, especially if it would increase the likelihood of successfully repeating the experiment. The experimental procedure should be described in present tense and describe steps actively. For example “Stock solutions and reaction mixtures were prepared under anaerobic conditions, using an MBraun glove box" should be presented as "Prepare stock solutions and reaction mixtures under anaerobic conditions, using an MBraun glove box.".
In this section, authors should provide:
- Images and videos for crucial and difficult steps to aid the researcher reading the method in successfully executing the protocol;
- Representative example(s) of data to illustrate the type of results obtained. We would like to encourage authors to submit original results obtained from scientific software and tools (e.g., Excel and ImageJ) and avoid performing misleading manipulations of the data (e.g., artificial enhancement of specific image features using graphic software like Adobe Illustrator and Photoshop).
- Data analysis
In this section, authors should provide information about data processing and analysis, including any statistical tests applied, criteria for data inclusion or exclusion, and details of replicates, including independent experiments.
- Notes
In addition to specific remarks included in the "Procedure" section itself, authors are encouraged to provide general notes that are relevant to the protocol, such as:
- Notes about reproducibility and variability in your experience;
- Additional notes, technical tips, and cautionary points that may improve the procedure.
- Recipes
We request authors to be precise about the ingredients they use (e.g., buffers and media) and the storage conditions and shelf life of each solution. Note that minor details in this section (such as catalog number of a reagent, or the type of water used), when not precisely followed, often lead to the failure of an experiment. Authors should indicate whether any materials are subject to Material Transfer Agreements (MTAs).
- Acknowledgments
Authors are expected to acknowledge funding sources that have supported their work. If the protocol was adapted or modified from previous work, please acknowledge the previous work here as well. Authors should use this section to declare any conflicts of interest or competing interests that may impact the design and implementation of their protocol.
- References
Authors are encouraged to cite at least one of their own publications or preprints where the protocol described was used successfully in the past. In addition, authors are requested to include citations for all relevant literature. It is not necessary to format the reference list as this will be taken care of by the Bio-101 editing team. An example of the Bio-101 reference format is:
Bindschedler, L. V., Dewdney, J., Blee, K. A., Stone, J. M., Asai, T., Plotnikov, J., Denoux, C., Hayes, T., Gerrish, C., Davies, D. R., Ausubel, F. M. and Bolwell, G. P. (2006). Peroxidase-dependent apoplastic oxidative burst in Arabidopsis required for pathogen resistance. Plant J 47(6): 851-863.
Figures, Videos, and Tables
Figures: For initial submissions, Bio-101 encourages authors to embed figures in the text file (except for figures that are included in a composite PDF).
Image files should not be manipulated in any way that could result in misinterpreting the original image. Please refer to 'What's in a picture? The temptation of image manipulation' by Rossner and Yamada (Journal of Cell Biology, 166:11) for examples of inappropriate manipulation and valuable guidance on acceptable practices.
Videos: For video, a typical smartphone camera is adequate as long as the video is clear. Bio-101 requires that standard video formats be used (e.g., MOV, MPEG, AVI). Authors are strongly encouraged to include video recordings of procedures when possible as these can greatly improve the clarity of the protocol for students and other early-career scientists.
Tables: Tables should be numbered chronologically as they appear in the protocol, and should appear after the first time they are cited in the text. There are no limits on table size; the Bio-101 editing team will either adjust their size appropriately for optimal online presentation or advise the author to include them as a supplementary file if they are too large.
All figures, videos, and tables should be accompanied by an accurate and relevant title and legend.
Nomenclature
The use of standard scientific nomenclature is required. Species, genes, genotypes, and mutations should be italicized. Genetic databases for the species of interest should be consulted to ensure that the recommended names are used. Bio-101 encourages authors to refer to organisms by their common name (if a common name applies), and to provide the Latin name in parentheses at first use. Authors should ensure that the nomenclature they have used conforms to accepted community standards of the relevant discipline.