Collaboration is essential on many projects. However, collaborations can be difficult to navigate, so it's worth setting out expectations up front.

Proposing collaborations

We don't have an formal process for initiating collaborations. Emailing or setting up a meeting is sufficient. We will evaluate our available time and the effort required for the proposed project, and decide whether the project is feasible.

Project samples

For us to receive murine or other model organism samples, we will require acknowledgement that the animals are maintained and treated under an approved IUCAC protocol. Human samples are more challenging. If you have collected the samples and will be providing them with study IDs only and no PHI, we will need an agreement to that effect. We will use this agreement to get a non-engagement determination from our IRB. However, this may change in the future if the Common Rule is revised. If you are from outside of our institution, we require a Material Transfer Agreement before we receive any samples. If you are transferring us human samples, the MTA must specify that you will maintain all data keys and we will receive only coded samples. We will also need a copy of the IRB approval for the project, including the approved consent and protocols. This processes are time consuming, so we highly recommend that you contact us early to begin the process.

Project costs

Labs are not free, and neither are the people that work in them. We often can help generate preliminary data and assist in grant writing. However, larger scale investments will require funds to cover the costs of associated reagents and time investment for individuals offering part of their effort. This would mean any associated lab consumables, any kits required for sequencing library prep, and the cost of sequencing itself. Time-wise I often cannot offer assistance beyond 10-20% from any lab member, and then only when it is covered by grants. This is particularly important for sequencing projects. It is unlikely we would be able to cover the cost any project sequencing for preliminary data. If it is worth the effort, we may assist in generating sequencing libraries that you can submit to the sequencing core.

What about just one lane of sequencing?

Unfortunately, no. Everyone wants just one lane of sequencing for their project. But they are not free; it just means we'd be paying for it. This is very unlikely to happen.

Grant deadlines and meeting abstracts

Everyone has deadlines. Contacting us at the last minute is unlikely to result in our inclusion on a grant. Again, let us know early if you would like our assistance in writing a grant, a letter of support, or inclusion in the proposed study. For letters of support, a draft is required, which should include the grant title, mechanism number, mechanism title, and basic info of how we could help. All grants that might include us must be agreed upon ahead of time. I cannot be part of any grant without prior approval from our grants and contracts office. This is also a time consuming procedure, and they would require budget info and drafts well ahead of your actual submission date. The same principles apply to meeting abstracts. Let us know well ahead of time if any collaborative work is going to be presented. We have to agree to any abstracts that include data we generated.

Authorship and author order

We follow Guidelines for Authorship. This seems obvious, but sometimes it does cause issues. Based on these guidelines, authorship is assigned based on effort. Essentially you must have made an intellectual contribution to paper to be on it. Things that do not grant authorship: These are meant to be illustrative, not exhaustive examples. An important side-effect of these guidelines is that initiating a project does not guarantee first-authorship from your lab. If an postdoc A from your lab collects samples over two days, and postdoc B from my lab generates and analyses the data for 6 months, postdoc B will be first author.

Open science and data sharing

We value openess in our work. It's critical to reproducibility and open science accelerates discovery. For us, this means even PCR primers will not be available by request. "By request" mostly ends up being not available. If we perform analysis, the code will most likely end up on our public lab code repository. Anyone will be able to see, download, and use this info. Sequencing data from model organisms will be deposited into the Sequence Read Archive no later than coincident with publication. For human data, samples must have proper consent and sequencing data will be deposited into the dbGAP general collection. We also support preprints, and will strongly urge the deposition of finished drafts into a preprint server such as BioRXiv or PeerJ Preprints. Depending on publication venues, sometimes preprints are not possible.