Publication Guidelines

1.a. Apply criteria (below) to determine whether work memorialized in research and review articles, as well as book chapters, was related to JBEI. These criteria apply to research and writing phases of publication. Authors should consult with their Vice Presidents to ensure JBEI-related acknowledgments are appropriately included in publications. If work meets any of the following criteria, then publication should be considered JBEI-related and include JBEI’s DOE acknowledgement (see 1.b.):

• • • Work performed by staff, during which allocated time was compensated by JBEI, regardless of salary percentage level or whether research had been started prior to arrival at JBEI.

    • Work performed by staff on specific tasks (below) that advance JBEI’s biomass-to-biofuels research mission, regardless of whether staff’s allocated time was compensated by JBEI:

      • • Feedstocks: cell wall biosynthesis, cell-wall engineering, systems biology, grass genetics

        • Deconstruction: enzyme optimization, biomass pretreatment, biomass materials, microbial communities

        • Fuels synthesis: biofuels pathways, metabolic engineering, biofuels transporters and toxicity, host engineering, synthetic biology

        • Technologies: sample preparation, enzymology, omics, physical analysis, bioinformatics, informatics

1.b. Include DOE acknowledgment for JBEI-related work (see 1.a.). JBEI is required to include a DOE acknowledgment in both research and review articles that are related to JBEI. LBNL's Regulations and Procedures Manual articulates this requirement in section §5.02 Scientific and Technical Publications. The following is JBEI's standardized language to acknowledge DOE support for research and review publications, as well as book chapters:

• • • “This work was part of the DOE Joint BioEnergy Institute (http:// www.jbei.org) supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.”

1.c. Include JGI acknowledgement – for those in the DOE Joint Genome Institute (JGI) User Community – whose research benefited from JGI's work. JGI's Deputy Director Jim Bristow asked that, since JGI is funded by U.S. tax dollars, we include an acknowledgment of this support in every publication that has been enabled with information that JGI has generated. Additional details can be found at JGI’s website, under Publication Policy. If you have any questions/concerns, please do not hesitate to contact Jim Bristow (jbristow@lbl.gov, 925-296-5609). Please include the following language in the acknowledgment section of your publication (e.g., journal articles, letters to the editor, reviews, posters) and on any other communications vehicles that you use to convey your research:

• • "This work conducted by the Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231."

1.d. Include EMSL acknowledgement - for those in the DOE Environmental Molecular Sciences Laboratory (EMSL) User Community - please be sure to acknowledge the access and use of EMSL facilities. Please include the following language in the acknowledgment section of your publication (e.g., journal articles, letters to the editor, reviews, posters) and on any other communications vehicles that you use to convey your research:

• • "This work conducted by the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at PNNL."

2.a. Submit publications (e.g., journal articles, letters to the editor, reviews, etc.) to Vice Presidents to review content and ensure appropriate authors have been identified prior to submission to journal. If an abstract, presentation, or a poster, a Director can serve as the approving authority. This action is the responsibility of the senior author.

2.b. Ensure that all authors listed on the publication are aware of the manuscript and are given sufficient time to review the manuscript prior to submission to publisher or conference coordinator. This action is the responsibility of the senior author.

2.c. Ensure, when researchers from other JBEI Divisions are co-authors, that appropriate Directors and Vice Presidents from these respective Divisions are notified of the manuscript prior to submission and given time to review the manuscript. Directors and Vice Presidents will be included as authors on the manuscript as appropriate and in accordance with the journal's policy. This action is the responsibility of the senior author.

3.a. Contact JBEI’s Liaison (Robin Johnston, RJohnston@lbl.gov, 510-486-5947) to LBNL's Technology Transfer and Intellectual Property Management Group for guidance prior to submission to journal, if the manuscript contains patentable material. Please do this before any public disclosure, in order to prevent the loss of any rights to your work. You may be entitled to royalties on any inventions or processes described in your paper.

3.b. Ensure Vice Presidents review publications (e.g., journal articles, letters to the editor, reviews, etc.) before submitted to journal to scan for intellectual property equities. If an abstract, presentation, or poster, submit to Director to determine whether publication contains patentable material. If there is patentable material, Director will alert appropriate Vice President, who will direct you to contact JBEI’s Liaison (Robin Johnston, RJohnston@lbl.gov, 510-486-5947) to LBNL's Technology Transfer and Intellectual Property Management Group.

3.c. File a Record of Invention Form, if your paper includes patentable material. For more information, contact JBEI’s Liaison (Robin Johnston, RJohnston@lbl.gov, 510-486-5947) to LBNL's Technology Transfer and Intellectual Property Management Group.

3.d. Visit LBNL's Technology Transfer and Intellectual Property Management Group for additional information.

4.a. JBEI policy states that all federally funded published strains/plasmids/parts/seeds should have entries associated with them in the private JBEI registry (strains associated with JBEI Strain Archive samples) as well as in the public JBEI registry.  

4.b. The first author on the paper is responsible for depositing the strains/plasmids/parts/seeds and associated information ideally prior to submitting the paper for publication, or no later than immediately after the paper has been published. The first author will need to create a folder containing all the strains (newly synthesized or existing strains) mentioned in the paper within the JBEI private registry. This will then be translated into a link for the public registry to be cited in the paper or shared for the public.

4.c.  The following links are detailed instructions for sequential steps needed to obtain a link to the public registry:

• • Submitting and Creating Strain Entries for Publication Link

5.a. Proofread your publication for spelling, grammar, and punctuation.

5.b. Check all formatting and scientific notation or illustrations for accuracy.

5.c. Ensure all references are in the format required by the publisher.

5.d. Save your document in a generic format (e.g., .doc or .rtf), prior to submitting to journal. Save a back up copy in a JBEI shared folder. Do not post this version of your publication to an external website or distribute to colleagues outside LBNL or your author list, until you have received a release from LBNL's Technology Transfer and Intellectual Property Management Group.

6.a. Reach an agreement with the editors and incorporate any agreed upon changes into your final document that comes out of a peer review process. These changes are part of the qualitative scientific review of the paper and are an essential aspect of scientific scholarly publishing. If your publisher does not have a peer review process, email a copy of the final version of publication submitted to journal to JBEI’s Operations Division (Jasmine Smith) for reports coordination.

7.a. Email a copy of final version of publication submitted to journal to JBEI’s Operations Division (Leah Freeman Sloan) for reports coordination.

7.b. Note: All scientific and technical reports authored at LBNL, at any LBNL located user-facility, or authored in collaboration with other facilities or laboratories, must be submitted to the Report Coordination Office (RCO). RCO’s mission is to support the acceleration of scientific discovery through the collection and dissemination of scientific and technical works authored at LBNL. The submission of reports is required by the DOE/UC contract. Furthermore, LBNL's Regulations and Procedures Manual articulates this requirement in section §5.02 Scientific and Technical Publications. This is the case even if the other facility or laboratory has led the collaboration.

8.a. JBEI Operations assists researchers in managing payment of publishing charges (i.e., submission fees, page-related charges, article reprints and preprints).

8.b. Each JBEI research division is responsible for payment of publishing charges from their division's budget.

8.c. If you receive an invoice requiring payment for publications charges, please submit the invoice to this form as soon as possible.