I am thrilled to say that after two years of work, my paper has been successfully published and I am first-author of a peer-reviewed academic paper, accepted for publication with minimal revision!

Over these past two years, I learned the ins and outs of proper experimental procedures, statistical analysis, and manuscript development, and now I can share tips from my own experience on how to publish in S.T.E.M.

From conducting an expansive literature review, designing and executing a full-factorial greenhouse trial, utilizing laboratory procedures to examine the growth and productivity metrics of my study species, learning how to use SPSS and R software to analyze my statistics, and ultimately publishing my manuscript, each step had its own challenges and rewards. Here, I break down the steps I took to help you organize your own research and guide you towards publishing your own academic paper.

Step 1: Choose Your Team

Publishing was one of the most challenging tasks I have undertaken to this date, but it would not have been possible if not for the strong team of scientists I had working on this with me. The unwavering support and assistance of my co-authors is what brought this paper together. For your first publication, I strongly suggest joining a lab from your university or collaborating with other individuals that have experience in the field you wish to publish in.

Step 2: Researching Your Topic

Prior to planning an experimental design, it is crucial to read the work of others on your chosen topic. Getting as much background information as possible will assist you with planning your study, getting an understanding of which metrics you should record, and learning about what previous studies have found. This assists with building the blueprints for your design.

Step 3: Plan and Execute Your Experimental Design

At this point, you need to have set a specific research question, created a design, and allotted specific deadlines and time budgets. In this article, I go in-depth on all of these points. This is where you need to collect as much data as possible. Remember, it is likely you will not use all of the data, but the more you collect the more options you have to work with when analyzing your statistics. When conducting your statistical analyses, ensure that you are comfortable with whichever software you will be using to analyze your work. Sites such as Youtube and Linda.com offer a vast array of tutorials to help familiarize you with these software packages.

Step 4: Manuscript Preparation

When it comes to manuscripts, each journal has a specific style and guidelines you must adhere to. Research “instructions for authors” for multiple peer-reviewed journals and see what their criteria include. When choosing a journal, it is important to consider the impact factor, which is the number of times that a paper from the journal gets cited on average. Certain journals have incredibly high impact factors, but this in turn means that they have a lower acceptance rate which is another critical point to consider. After selecting a journal, follow their guidelines. They will have specific requirements that are important to adhere to in order to increase the likelihood of having your paper accepted for review. It is at this stage that you should choose the order of authorship on the paper, and who should be the first author of the paper. This order is typically established by order of contribution to the paper.

Step 5: The Editing Stage

This will probably be one of your longest and most challenging stages. My lab and I spent many months going back and forth on researching, writing, editing and then editing some more. There will be days when you spend hours researching just to write one sentence. There will be days when pages worth of work will be crossed out and you will have to start again (and again and again). Graphs and figures will have to be tweaked and possibly reworked. During the editing stage, the most important thing is to maintain perseverance and to take it a day at a time.

Step 6: The Submission Process

When your manuscript has been edited to the satisfaction of everyone on your team and is ready for submission to your journal of choice, there are several critical documents you must submit; your manuscript, a cover letter to the editorial committee, your figures, and possibly your code if you used a software such as R. You will need to make an account with the journal and submit everything they require within their formatting guidelines. Make sure to research how to write a cover letter for a manuscript, as it is entirely different from one you would submit for a job posting. As well, it is a good idea to set up an ORCid, a unique code to identify scientific and other academic authors to keep all of your contributions organized, and link it to your paper.

Step 7: The Peer Review Stage and the Revision process

After submitting your manuscript, if the editorial board chooses to accept your paper, it will be sent to a committee of peer-reviewers. This may take between several weeks to several months. The peer-reviewers will provide feedback on your paper, which is essentially another round of edits. From the number of changes they request, you may either have minimal revision or possibly have to redo certain sections. This is one of the final hurdles, put in your best work and polish it according to the guidelines from the peer reviewers.

Step 8: Accepted for Publication – Choosing Between Open Source vs. Copyright Transfer

Once accepted for publication, you will have 2 options: leave your paper as open-source or transfer the copyright over to the journal. Open source publications are openly available to viewers but can cost the publishing authors upwards of several thousand dollars. Copyright transfers typically have no cost involved with the publication, but viewers must read the paper either through an institutional proxy or by subscribing to the journal. Both options are valid, so choose whichever is most practical for you and your team.

Step 9: Final Revisions from the Journal

As you come close to publication, the journal will send you a proof with a list of final revisions. These are typically the last changes you can make to your paper, so ensure that everything is as you want it to be.

Step 10: Publication

This is the finish line, and once you have passed it, you are done! It takes time and effort, but once you are published, you are officially an author! Make sure to keep a balance during this process, talk to your family and friends, spend time on your hobbies, and ensure that you have downtime. Ultimately, it will all come together.

After a 2 month growing and censusing period, followed by a harvesting, drying, and biomass census I have concluded my 200 pot competition series.
During this period, I had obtained a photometer to measure light levels and did two light census for both the overall pot as well as below canopy. I am hoping that these light measures will provide quantifiable insight on the effect light has on growth. I hypothesize that plants receiving ambient light will yield greater mean biomass per species, while those in shade conditions (to mimic shrub presence) will have a greater mean height due to leggy growth.
I wanted to quantify the growth of my plants through several metrics, and therefore chose to obtain both height and leaf measurements for each species from each pot. In order to acquire these measurements, I implemented a new censusing technique for my second and final census. In this census I counted the number of individuals of each separate species there were per pot. Following this, I took the tallest individual of each species, and recorded its height along with the number of leaves. This way, following the harvest and mechanical oven drying period I would be able to compare the biomass of the plant with its height and leaf count. This would allow me to evaluate plant growth using two separate dimensions; plant height along and number of leaves vs. plant biomass.

After using a mechanical drying oven set to 62 degrees Fahrenheit for 48 hours, I used a precision scale to obtain the biomass of each plant.

The experiment planning, seed counting, pot filling, plant censusing, harvesting, and biomass analysis processing were extensive processes. I am extraordinarily grateful to Dr. Christopher Lortie, Dr.Jacob Lucero, Masters graduate Jenna Braun, research practicum student Anuja, and Economics and Finance student Denis Karasik for their time, efforts, and immense assistance with running this experiment.

Statistical analyses for all of the results are still in work, and I am eager to see the conclusion my experiment comes to

I want my final paper to be useful for and applicable to restoration ecology.  This led me to inquire what data I should collect for my second census. My germination rates are up, and all four species are present, so would relying on number of individuals and biomass of each species per pot be enough data? I decided that since I am using light as a limiting factor I must include height in my data; the plants may have somewhat similar biomass, but if it is due to leggy growth in the shaded pots then it will be important to note that although biomass was similar resource allocation was not equal. Are great amounts of leggy, weak, and nutrient deficient plants with few leaves better for ecosystems then having fewer shorter but thicker, more leafy plants?  I measured the number of individuals per species per pot, alongside with the height and number of leaves the tallest member of each species had per pot. I have yet to analyze these numbers, but did notice trends when doing the census!

Side note: I conducted a germination experiment in the greenhouse prior to using these seeds, and have let them grow out. My Phacelia tanacetifolia is growing a beautiful flower!

Salvia columbariae, Phacelia tanacetifolia, and Plantago insularis are key phytometers (plants that indicate ecosystem conditions) in the San Joaquin Desert of California. As the highly invasive exotic Bromus madritensis colonizes in this non-native environment it lacks the environmental suppressors and competitors it faces in its native habitat. This leads to native Californian desert ecosystems to shift to a new model where native plants are excluded due to competitive disadvantages. decreases in native biodiversity are directly correlated to the health of an ecosystem, ecosystem services, resiliency to climate change, as well as the resources and for these reasons, identifying methods of restoration ecology is crucial.

Using my 3 factor (ambient light vs shaded conditions, low vs high B.madritensisdensity, native seeds at 6 levels of density (0,3,6,9,15, or 30 natives)) greenhouse competition trials I aim to identify what density of native species must present in a pot with a surface area of 153cm²  to outcompete an exotic one.I have previously run an experiment to identify optimal density in pots of the same surface area using each of the native species in monoculture, implementing the same light versus shade conditions with a total of 365 replicates. I will assess if I am able to compare these differences in optimal monoculture mix density to a polyculture mix with invader presence. If my data finds an optimal density using these methods, I hope to further my research and apply my findings to population ecology by estimating necessary population metrics required to apply this to ecosystem for large scale restoration and contribute it towards field work.

My experiment currently contains 200 pots, 100 of which are shaded by a bamboo structure I suspended. Germination has begun, yet it is still difficult to differentiate among species this early on. As predicted, the shaded individuals have demonstrated leggy growth as they reach towards the light source, yet there seems to be leaf production in possibly higher concentrations in the shaded pots than the ones experiencing ambient light. It appears that the shaded pots have a higher germination and growth rate (measured by number of individuals and number of leaves per pot). Is it possible that the shade-preferring B.madritensis is facilitating growth through positive density dependence? Am I witnessing an Allee effect in the form of environmental conditioning? Or is the answer as simple as light levels in the shaded conditions being sufficient for the natives as well as B.madritensis? Using the metrics of germination of species per pot as well as leaves per species and finally above ground biomass at the end of my experiment I will continually assess success through the different factors and levels I have designed and implemented in my experiment and hope to achieve a successful conclusion.