Journal Scope and Content

BioTreks is an open access peer reviewed journal for high school-based synthetic biology research.  Each year, students are invited to submit original work detailing their research designs, laboratory results, and personal perspectives on synthetic biology and education. In April, the authors present the drafts of their papers at an online conference for discussion and review by their peers.  Following the conference, the students perfect their manuscripts based on the feedback and questions they receive from conference attendees.  A detailed schedule of the current publication cycle can be found here.

BioTreks articles are prepared and published in one of four formats depending on their content.  These formats are separately defined for Design, Research, Methods, and Perspectives Articles.

  • Design Articles.  Synthetic biology is about taking a top-down approach to engineering biological systems that serve a social or environmental problem.  Successful synthetic biology projects generally start by considering what the solution is going to look like on the system, device, and part levels.  Design Articles provide opportunities for teams to carefully consider and describe each of these project components before beginning their lab work.
  • Lab Reports.  Lab Reports should describe the results of at least one complete experiment and draw meaningful conclusions based on these results.  It is perfectly acceptable for an article to describe research that reproduces the work of others so long as the work is referenced in the manuscript.  Articles that report negative results and failed experiments are also welcomed, provided the authors are able to draw meaningful insights from the results.
  • Methods Articles.  These submissions provide detailed procedures and tips for performing standard synthetic biology techniques or assays.  The purpose of Methods Articles is to guide others in using techniques that have been successfully applied and mastered by the authors in their own high school labs.
  • Perspectives Articles.  Perspectives Articles provide free-flowing commentary on a wide range of topics related to performing synthetic biology research and education in high schools.  These manuscripts do not follow a rigid format and are divided into sections based on the authors’ needs.  Perspectives Articles are well suited for presenting new ideas and reviews of books and technologies that do not document hands-on laboratory work.

The Publication Process

The BioTreks publication process generally consists of eight steps, which begin with the authors submitting an abstract for presentation at the annual conference and end with the article being published online.  Each of this steps is briefly described below.

  • Abstract Submission.  The process begins by students submitting abstracts for papers that they would like to present at the BioTreks conference and publish in the online journal. The abstract submissions will generally provide the title followed by a list of authors and a brief description of the work.  The submission also indicates whether the students plan on preparing a Lab Report, or Design, Method, or Perspective Article.
  • Manuscript preparation.  After submitting an abstract, the students begin the process of preparing their manuscript for presentation at the BioTreks conference.  This is accomplished by drafting the manuscript directly on Breezio or preparing it offline and uploading it to Breezio when finished.  It doesn’t matter how the manuscript is written, so long as a complete manuscript with accompanying video, figures, and tables is ready to be shared with other participants in advance of the online conference.
  • Peer review.  Peer review is an important part of scientific publication.  The process generally involves impartial experts in the field reviewing the author’s submission for accuracy and completeness.  When preparing a paper for publication in BioTreks, peer review actually takes place during the online conference, when students, mentors, and experts read and discuss the manuscripts that the students have posted online.  During the online conference you will most likely be participating as an author of your own work and a peer reviewer of everyone else’s work.
  • Author revisions.  Following the conference, authors will have about a month to modify and improve their submissions based on the questions and feedback they receive from students, teachers, and scientists at the conference.  It is important that, as an author, you take advantage of this time to make any necessary corrections to your manuscript.

Caution: In the month following the online conference, authors are expected to respond to every one of the reviewers comments by detailing how the authors addressed the readers’ concerns in the revised manuscript or explaining why the authors have decided not to follow a reader’s suggestion.  Failure to adequately address all comment may result in the paper being rejected for publication in the journal.

  • Editorial review.  At the end of the revision period, the student manuscripts will be locked down and the BioTreks judges will review the documents to decide which are acceptable for publication.  Papers will generally be deemed acceptable for publication, provided the authors have explicitly and adequately addressed EACH of reviewers’ comments and adhered to all formatting requirements, as described below.  During their review, the judges will also award badges to those articles which excel in key areas of peer review.
  • Copy editing.  Copy editing involves checking the manuscript for grammatical errors and reformatting it to fit the journal style. This is also the point at which the figures and tables are inserted within the body of the text. Copy editing will be performed by BioTreks staff between July and September.
  • Author review.  Following copy editing, the authors will receive a pdf-formatted proof of the final article and be given a chance to identify any last-minute mistakes that may have been introduced during the copy edit process.  At this point the authors are only permitted to recommend minor edits to the article.
  • Publication.  The completed articles will published online as part of the current issue of BioTreks.

Manuscript Sections

Manuscripts should be organized into sections according to whether the material is intended to be published as a (L)ab Report, or (D)esign, (M)ethod, or (P)erspective Article.  Excellent examples for of each of these formats can be found among the papers published in previous years.  The different sections are described below in the order in which they should appear in the manuscripts.

  • Title (D, L, M, P).  The title should concisely summarize the paper and any significant conclusions.
  • Authors (D, L, M, P).  The comma-delimited names of authors should be listed in order of their contributions to the study.  Also place an asterisks after the author’s name who will serve as the primary contact for the team.
  • Affiliations (D, L, M, P). Provide a comma-delimited list of the organizations with which the authors are affiliated. In most cases the Affiliations section will simply be the name of the school that you attend.
  • Abstract (D, L, M, P).  The abstract should summarize the article in less than 300 words by briefly touching on the key points covered in the background, methods, results, conclusions sections of research papers.  Similarly, the abstract for design, methods, and perspectives papers should summarize the content addressed in each of its major sections.

Caution: The abstract cannot contain any figures, tables, or citations of referenced literature.

  • Video (D, L, M, P). Each manuscript should be accompanied by a short video in which the authors briefly describe the motivations, methodologies, and results of their project. The video is intended to give conference attendees and prospective readers a brief overview of the student project and encourage them to read the article.  This section of the manuscript will provide a link to the video, which will be posted on Breezio.
  • Keywords (D, L, M, P). List 3-5 comma-delimited words or phrases that will help locate the article in a search.
  • Background (D, L, M).  The background section describes the experimental objectives and why they are important.  This section will generally start by describing the big problem that the researchers are trying to solve, how they plan to go about doing this, and how the current experiment will support this process. In the case of Student Artwork, the background section describes the context and motivation for the artwork.  Remember to cite all sources of information used here or elsewhere in the paper.  See the Reference section for more details.
  • Systems Level (D). Design Papers should contain a section which describes the team’s solution in the context of the complete biological system.  This section deals with how the system works as a whole.
  • Device Level (D). In Design Papers, the Device Level section addresses the key functional components of the system.  Devices would include the engineered organisms and any functional pathways that are required for these organisms to perform their jobs.
  • Parts Level (D).  The Parts Level section of a Design Paper shows how specific genetic components are to be combined to make the functional operons pathways described in the previous section.
  • Safety (D). Design Papers should also include a brief discussion about how the proposed system will be safely constructed, tested, and employed to avoid harm to the developers, users, community, and environment.
  • Materials and Methods (L).  This section is designed to tell other researchers everything they need to know to reproduce the reported experiment.  It accomplishes this by providing a brief but detailed description of the various procedures that were followed when conducting the reported experiments.  It also details the materials that were used and often lists the supplier of these materials in parenthesis.  The Materials and Methods section should also contain a subsection that details the team’s approaches to laboratory and environmental safety.

Caution: The Materials and Methods section should not contain numbered or bulleted lists.  All procedures should be described in concise paragraphs with the manufacturers of critical reagents and kits named in parenthesis.  When following a protocol that accompanies a commercial kit, it’s generally sufficient to indicate that the assay was performed “in accordance with the manufacturer’s protocol.”

  • Requirements (M). A requirements section should be included with all methods manuscripts to describe in separate subsections, the time, equipment, supply, and reagent requirements for the described procedure.  The purpose of this section is to help the reader assess whether they have access to the necessary resources for performing the procedures.
  • Procedures (M). The procedures section of a methods paper generally details the processes involved in performing a particular technique as nested lists of the individually numbered steps.
  • Notes (M).  The notes section is also unique to methods papers and is used to provide tips and suggestions regarding the performance of different steps in the procedure.  This section consists of a numbered series of notes which are specifically referenced in the procedures sections as Note 1, Note 2, Note 3, etc…
  • Results (L). This section is used to describe the results of the reported laboratory study.  Results sections are generally arranged in subsections according each set of experimental outcomes.  Subsection titles should concisely state the conclusions that can be drawn from the reported data.  Each section is generally accompanied by one or more figures or tables to help the reader understand and interpret the data reported in this section.
  • Discussions (D, L, M).  In Research Papers, the Discussions section gives the authors an opportunity to summarize their experimental results and describe how they met or failed to meet study objectives.  In a Research Paper, the Discussions section should conclude with a consideration of what additional experiments will need to be performed to carry the project forward.  When written for a Methods Paper, the Discussions section should be used to summaries advantages and shortcomings of the method and suggest ways for improving the process.
  • Body (P).  The main body of Perspectives Papers replace the Background, Materials and Methods, Results, and Discussions sections of research articles with content that is organized into sections and subsections of the authors’ choosing.  In this way, Perspectives Papers read more like a magazine article than a scientific research paper.
  • Acknowledgements (D, L, M, P).  This section generally consists of one or two brief paragraphs which recognize individuals and organizations who made the reported study possible through the contribution of knowledge, insights, or material resources.
  • References (D, L, M, P).  This section consists of a formatted list of all publications referenced elsewhere in the article.  The citations are referenced throughout the text and listed in this section according to the standards set out in Citing Medicine, 2nd edition: The NLM Style Guide for Authors, Editors, and Publishers.
  • Featured Image (D, L, M, P).  Authors are invited to submit a high resolution graphic which highlights the main point of their paper and can be displayed alongside the title in the journal’s table of contents.  Featured images provide an important way to attract a reader’s interest in your article.

Tables and Figures

Authors are encouraged to include tables and figures as a means of directly supporting the points that they are trying to make in the text.  All tables and figures must be specifically cited in the text (i.e. see Table 1, see Figure 1) and should be placed just after the paragraph where they are first referenced.

Figures should imported into Breezio as high resolution images and be accompanied by a descriptive caption, which is added as inline text immediately following the imported image.  Each caption should begin with the figure number (i.e. “Figure 1”) and start with a sentence which summarizes the main point of the figure.

Caution: All figures must adhere to the following standards for a manuscript to be published in BioTreks:

  • Graphics must be the original work of the authors or used with the expressed written permission of the copyright holder.
  • Graphics must have a minimum resolution of 1200 dpi when rendered on the printed page.
  • All text that is contained in a graphic must remain legible when the image is rendered on a printed page.
  • Figure captions must completely describe the figure and its contents to the reader so that they can understand the graphic without reading the surrounding text.

Conclusions

This guide provides a brief overview of what can be a very confusing process, especially if you’ve never written a scientific paper before. We encourage you to search for for your favorite synthetic biology topics on http://pubmed.com to get a better idea of how scientific papers are generally written and organized.  Also, please remember that we’re here to help.  Simply use the Breezio interface to post a question alongside any of the sections you find confusing and we’ll do our best provide an answer.  Good luck and thanks for contributing!