Optimize Your LabArchives Electronic Notebook Setup for Collaboration and Data Integrity
Transcript
I'm Hannah Clark. I'm part of the LabArchives team. We're going to walk through some of the basics of LabArchives for this very first session, which is titled Optimize Your LabArchives Electronic Notebook Setup for Collaboration and Data Integrity.
So to start with some of the basics, I'd like to cover a couple of slides just to kind of talk about what is LabArchives. So at LabArchives, we actually have four different products. I'm going to be focusing on the first one, which is our ELN, or as Columbia First called it, an electronic research notebook used to securely store, search, and share research and scientific data.
Now, a lot of my examples today are going to come from the wet lab side of the world, because that's my personal background, but you can use it to communicate with your team about your projects. Now, we also have inventory, scheduler, and there are separate tools that are not currently part of the Columbia license, but the ELN for education has been in use at for many, many years now. It's going to be all the same tools and features we talk about today, but for course use.
So think of like a biology or chemistry based course where you have students completing assignments, that assignment is graded, and kind of that more preparing students for their future career in science side of the world. Now, what is a lab notebook? What is an electronic notebook? I like to think of LabArchives as more of a collaboration tool, right? It's for you and your colleagues to work together with your data, and our goal as a company is all about reproducibility. If I spend many years working on a project, I'm going to end up with a figure, figure four in our publication, and this publication, if someone ever looks back at it and says, hey, can you show me the data for figure four? Well, hopefully we can go back to a repository, we can go back to the supplemental data and find the related information.
But as we know, there is much more behind that work from methods, procedures, materials, equipment reservations, equipment calibrations, notes and observations, and discoveries along the way that are important intellectual property that prove that you're doing the good work that you're doing. So, I like to say it's more the story of your data, you know, everything from coming up with the idea all the way into sort of the publication of your work. If you don't have an account right now, you're welcome to make one.
Go to LabArchives.com, you'll see a single sign-on drop down where you'll log in with your Columbia credentials and get right into your notebook. Now, there are many permissions at LabArchives. The highest level role is that of the notebook owner.
Now, I would highly recommend that notebooks are owned by a central person, and more specifically, it should be whoever's responsible for that data. Usually a PI or supervisor, department head, someone who intends to be at Columbia for the sort of foreseeable future. Now, our PIs are lovely folks, they're very busy, they usually like to kind of delegate to other folks to kind of handle the day-to-day operations of the notebooks, and that's where those admin roles come in.
An admin can add data, can edit data, can invite people on behalf of that notebook owner. So, it's sort of your right-hand person. The other role there is user.
A user can add, they can edit, they can view and download. They can't share. So, they can't invite someone at NYU or Harvard or Duke or wherever.
They can simply work within the notebooks that they've been given access to. The other role there is guest. Now, guests might be undergraduate students, interns, volunteers, people outside of Columbia might be added in as a guest.
It's more for kind of short-term collaborations. And someone can have many different roles. Their roles can vary per notebook, and you can always change someone's role.
You can transfer ownership. It's very flexible on that front. Now, the talk for today, this first session, is all about notebook setup, and that really gets into the structure of your data and what makes the most sense.
Now, generally, I recommend taking a step back and looking at your work in the long term. So, if I look back at my data five, six, seven years from now, how would I find it? How would someone else find it? Would they know, oh, this is work by Hannah, so it's going to be in Hannah's notebook? Would they know, oh, this is work done in 2026, it's going to be in the 2026 notebook? Or, and I think this is more likely, would they know what project or process or, you know, trial was this part of? And that's often the most common in my experience, and that's why I generally recommend making notebooks on a project basis, right? All the related data goes into the same notebook. Now, we are always going to have data that doesn't fit into one project.
It could be procedures, policies, protocols, safety documentation, equipment maintenance policies, stuff that everyone needs, and you want to keep that documented, you want to keep that shared among the team, but it's not specific to one project. It might be the same, you know, tissue culture, fume hood is used in many different projects, but you need to keep track of the kind of maintenance of that equipment. Now, to give kind of two examples, so the left-hand side, this is a lab-wide notebook, where I have my ELN policy, maybe I have a copy of our data management and sharing plan, maybe I have our protocols, our templates, our policies, notes, weekly meetings, things like that.
Everyone can add to it, update it, it's shared across a whole group. Now, the right-hand side, I have more of a project-based notebook, where all the data related to a certain project is located. So, I might have the protocols that are relevant to that project, the samples related to that project, each of the experiments, and maybe there are different phases or goals within that project, so that it's a one-stop shop.
Everything related to that data is all together, everyone working on that project has access to it. Now, the reason I like the project-based structure, related data goes to the relevant notebook, related team members have access to the related notebook. So, let's say hypothetically our group has three notebooks, X, Y, and Z, all the related data goes to the right notebook.
If you're part of project X and Y, you're in those two notebooks. Project Z might be a little special, not everyone gets access to it, it's a little more kind of a privileged information, a more private project that not everyone's working on, so I can restrict access to that notebook. Now, very often, especially for our clinical folks, our shared services folks, our more core facility side of the world, a sequential notebook might be useful.
So, this could be a notebook per year, per business quarter, per semester, and if you have a very long-running project, lots of collaborators, lots of people working in it, the date can be helpful, right? So, I can go looking for data from 2023, it's going to be in the 2023 notebook. So, that can help if you've got very long-running work. Now, after today, if you attend all three sessions, you will be a lab archives expert, but if you have any questions after today, you are more than welcome to reach out to us.
So, of course, you have the excellent team on campus at Columbia to help answer questions, give guidance on policies, all that fun stuff, but you can also reach out to our support team. So, that would be support at labarchives.com. We also have a knowledge base, quick start guides, additional materials, and more. So, you can learn all about various tools and features.
So, I wanted to pause and see if there were any questions. We've had a lot of folks join the last couple of minutes. Welcome.
As a note, I think they mentioned earlier, the session is being recorded, and if you have any questions, you're welcome to use the chat panel. I'll keep an eye on that. There was a question, and I answered it in the chat, but maybe you wanted to discuss it a little bit.
Absolutely. So, reading this out for the room and also for the recording, the question is, is there a storage limit per user? So, and Jessica answered it, a lot of people, including Columbia, will describe the storage as unlimited, which more or less it is. I always add a big asterisk to that, because you always have, you know, the joke is, there's always someone with bigger data, because there is.
When you talk about your high performance computing folks, your large microscopy and sequencing folks, you have excellent resources. The research data team would love to chat with you about where to store that data, but for a lot of researchers, laptop crams might be all the storage you need. So, it's four gigs per individual file, so each individual attachment can be up to four gigs.
We generally recommend less than 30,000 entries per notebook, less than a terabyte per notebook, but what Jessica said is very true. We often say unlimited, because there's no limit to the number of pages, folders, notebooks, users. You can keep going as long as you need, though, you know, of course, if you start hitting a point where you have a need for high performance computing, what I usually say is, if you find that you're having to wait for your network to upload a file, and it's inconvenient for your workflow, there might be other ways.
There might be servers that are more physically located somewhere in Columbia, or broadly, maybe in New York, that are a little bit faster, that are more for your workflows. So, if you're all the big data folks, it doesn't necessarily mean you wouldn't use lab archives, it just means you'd have pointers out to the raw data, wherever that would be slurred. All right, any other questions on anything so far? All right, perfect.
All right, so let's talk about lab archives. So, what you're seeing on the screen here is a notebook. This is a notebook called Research Project ABCD.
We're going to talk about notebook setup, and creating folders, and permissions for today, or for this first session. Now, this is the notebook that I've had running for quite a while. At the top here, I have my data management and sharing plan, and the policy is from my lab on how we want the notebook to be used.
This is totally optional, but I think it's a nice way to have this information all together, because someone five years from now is going to look back at this notebook and say, wait, which grant was this part of? Who was working on this? What was the purpose of this? How were they naming those files? So, it's nice to have this sort of thing in a centrally shared place. Now, this notebook is more what I would call a workflow-based notebook. So, my group has lots of page templates that are preformatted, and anything in the in progress folder is in progress.
We're working on it currently, whereas things put into the completed folder are completed. So, I can really quickly see what's going on within my group, who's assigned to what. Maybe I have additional subfolders for each person in my group.
So, if the page is in in progress and in Hannah's folder, that means Hannah's working on it right now. So, the pages can obviously be moved, and copied, and updated as well. Ultimately, data is added to a page.
So, this is my page for Experiment 101. At the top here, I have the notes and steps for Experiment 101. It could be a procedure.
It could be observations. I might have materials as part of my experiment. And down here, I have some files.
Now, as mentioned, we can upload files of any file type, whether that's something we integrate with, like GraphPad and Snapseed, or things like images, office documents, PDFs, and even more proprietary file formats. So, if you have a unique piece of software for the equipment and tools you have, excellent. That data can certainly go into LabArchives.
Now, you'll notice on every entry, there's tools for working with these entries, and I'm going to talk about these more in a second. On the right-hand side, you see a date and time stamp. Now, when we talk about LabArchives, this is kind of the reason you would use LabArchives.
It gives you the ability to see exactly what was done, who did the work, what changes they made. You can review every single version of an entry. You can revert to earlier versions.
You can review them. You can undelete them if you need to. You have a full record of what was done, who did the work, when they did the work, and you can always go back and prove that you're doing the good work you're doing.
So, that's what you need. Now, I'm going to go and talk a little bit about how to make a notebook, how to establish some folders, and how to invite your colleagues. Before I do that, are there any questions so far? All right, let's see.
All right. So, at the word notebooks, you're going to see all the notebooks that you have access to. And in that you all are part of Columbia, there's a notebook that I don't have that you will, which is a site-wide notebook owned by the Columbia team that has some documentation for compliance and IRB and all that fun stuff.
So, do take a look at that. It's a great resource. So, that's going to be your read-only notebook you're going to see in the list.
At the plus icon here, you can make a new notebook. Now, we talked about before you might make a notebook for each project, each grant, each workflow with your team. So, let's say our team has a brand new funding for project Z. I'm going to make the project Z notebook.
Now, a lot of people want to start from scratch. I want a blank notebook with no folders. So, they'll pick that no option.
Some people like the project structure. So, to see what that would look like, the project structure gives me these folders here for protocols, a sample log, experimental data. If I use that lab-wide structure, it gives me more of what a lab-wide notebook might have.
Is there content within those folders, or are they empty? Yes. The question is, is there content in those folders? The folders are totally blank. It's just a couple of empty folders for you to kind of get an idea of what's possible.
Now, so, no pages, no entries, just a couple folders. Now, when I click create and confirm, I have a new notebook that I own. So, at the word notebooks, now you see I have four.
Now, if your group has been using lab archives for a while, you might go, hey, I have 30 notebooks. I'm not accessing the ones from 10 years ago. You can actually hide notebooks.
It's the option right here. We call it our notebook manager. So, you actually see I have a couple of hidden notebooks already.
These are things I don't go to as often, and you can unclick that included navigator so you still have them, still get to them. You just don't have to see them day to day, which is sometimes nice for groups who have lots of notebooks. The other thing to point out here is the clone button.
So, these are over here on the right-hand side, this little two squares button. This is going to create a full copy of everything. So, let's say the question before, I have some pages, folders, content, ready to go.
I want two of these notebooks that look the exact same. You can clone them. The nice thing about cloning, it copies everything in the notebook, all entries, all pages, all folders, and all permissions.
So, if your group has already been set up and going, you have a notebook that you like, you can clone it and put new data in for a new project, perhaps. Now, our project Z notebook, you see we have a couple of folders here for protocols, a sample log, and if you right click, you've got a lot of options with folders. So, you can add a new subfolder in there.
You can copy from this notebook or from another notebook. You can even rename. So, maybe I don't want this to be a sample log.
I want this to be SOPs, Standard Operating Procedures and Safety Documentation. Then click okay. So, now the folder is called SOPs and Safety Documentations.
Similarly, I can move folders around just by dragging and drop and even move them within another folder as kind of a subfolder there. Now, the folder structure is totally customizable to what you want to do, and I always recommend to groups to have a conversation with your team about what makes sense for your projects and for your notebooks. If you're joining a lab that's already been used in lab archives, the folder structure might be established, but you can always change it around.
So, if you jump in, you get started, you set up your notebooks, and then you go, I don't like this. I want to change it. You can.
You can rename things. You can move it around. Add new folders, new pages.
It's very flexible on that front. You can rename. You do see an option to delete.
Now, keep in mind, no entries, pages, or folders are ever permanently deleted. So, let's say I delete my references here. I don't see them on the main list of folders.
However, they're just right here in our deleted items bucket where I could always unbleed and bring it right back in the book. So, just keep that in mind. Nothing is ever permanently deleted.
Once it's in your notebook, it's part of that record from today forward. Now, I want to hop into talking a little bit about permissions before we talk a little bit about kind of adding some data to a notebook. I don't see any questions so far.
So, keep going. All right. So, in order to kind of set up a whole labs notebooks, I might repeat this process a handful of times.
I might make five, six, seven notebooks if I want to, or I might just start with one. Now, I can manage access at the notebook level, at the folder level, at the page level. Most of the time, access is at the notebook level, and that's generally what I would recommend.
To manage access for notebooks that you own, click your name and go down to account manager. Now, this shows the people in my group and the notebooks they have access to. So, if I have someone new, click the add person icon and type in their email.
Now, it's worth ringing up at Columbia. It seems like some of you all have many, many, many formats of your email. You can invite someone with whichever email address they prefer.
So, if it's a particular format, make sure that's the one you invite them with. If it's someone outside of Columbia, you can invite them as well. Obviously, make sure that's in line with compliance and the data use agreements that you have, but you can type in their email and pick their role.
So, I talked briefly about roles earlier, but I didn't explain the difference between account admin and notebook admin. So, an account admin is your right-hand person. They can add, they can edit, they can share everything in my account.
Every notebook that I own, they can make more notebooks for me. That is a person I trust with everything. Now, sometimes, maybe they're not responsible for everything.
Maybe they're just responsible for some of the projects. Maybe just project Z. Maybe just project ABC. Maybe both of them.
And you can pick. And it might be the case where they're an admin in one notebook or a user in another, right? They're not allowed to share our data management policies. Most people in your group, most lab techs, grad students, med students, researchers in your group will have the role of user.
They can add, they can edit, they can work. They can't share. So, they can't invite their friend down the hall.
They can't go invite someone at another institution. They can simply work within their data. Now, you'll notice I can also give you only access.
So, some groups do make a notebook per person, right? So, the Clark Lab has a notebook for Jim, Jill, and Johnny. Jim, he gets edit access to his own notebook, but you have access to Jill and Johnny's notebook. So, you can choose to kind of set that up as you see fit.
The last role there is guest. We do highlight there 60 days of editing access. This person would be invited with temporary editing access for just about two months to those two notebooks.
So, something to keep in mind. Now, I'm going to add test here as a user to these two notebooks and confirm. When you invite someone, if they don't have an account, they'll get an email saying, hey, you've been invited to an account.
Click on this link to make your account. They'll log in and have access to your notebook. If test was previously using LabArchives, they already have an account.
They would just log in and get access. As a little pro tip, whenever you invite someone, if they already have an account, you're going to see their first and last name listed. So, there you see Clark Hannah.
That's an activated account. She has set up that account. She's logged in.
Test here hasn't logged in yet. So, we know that because we don't see a first and last name. The reason I bring that up, if you ever do invite someone with the wrong format of their email, that can be a nice quick sign to say, oh, yep, wrong format.
Now, at any point, I can change someone's role. So, I can make them an admin, a user, a guest. And I can also remove someone's access.
So, test, ah, he's been the best graduate student in our group. We're very sad. He's graduating.
We're happy for him. But sad for us. Let's go ahead and remove his access.
Trash can icon confirmed. This removes their access to all notebooks that I own. Now, let's say they're leaving our group, but they're still at Columbia.
That's great. They can go work on their other notebooks with their new lab or maybe their new PI and setting up their own notebooks. They can do that.
If someone is leaving your institution, obviously, make sure their access is updated. But you can also click the notebook icon to see which notebooks they have access to. So, my other account here is a notebook admin and just one of my notebooks.
Now, most PIs, most supervisors, account managers is how they manage access. It's real quick. One click, add someone to several notebooks.
Some groups want to manage access on a smaller basis. So, maybe I want to share just our brand new notebook here. Project Z. Triple dot menu, go down to notebook settings.
There are some settings you can adjust. I'll talk more about page signing and witnessing later on. Under user management, here are the people who currently have access to our Project Z notebook.
If I want to add someone new, click new user and invite them. So, I'm going to go back. Test, we're so excited he's returned.
So, we're going to invite them to this one notebook and confirm. So, Test is back. He has access to this one notebook.
He does not have access to the other notebooks in my account, just that one. And again, I can adjust his role to this one notebook if I want to. Now, an important thing to point out is this button right here.
Ownership transfer. So, as you mentioned at the very start, notebook owner is the highest role. Generally, that should be PIs, supervisors, managers.
And very often, PIs like to delegate the responsibility of setting up the notebooks to someone else. Maybe it's yourself, and that's why you're on the call. Welcome.
We're happy to have you. Feel free. Make your notebook, set things up.
Within a couple days, a couple weeks, I recommend transferring ownership to the PI or at least to a central person. Because sometimes we have grad students who go in and make a bunch of notebooks, add a whole bunch of data, all working great. They graduate, they move on, and they forgot they still own that notebook.
And that happens. It's no big deal. We can take care of it.
Reach out to your site administrators. It's like three clicks to fix. But I recommend just to take something off your plate for graduation day, go ahead and transfer ownership.
And no matter what, no matter whether you use web archives or other tools, I would always recommend that your PI has access to your data. Whether they use it, whether they look in and take a look is up to them. But definitely make sure they at least have access to your work and know where it's being stored.
Because they should. Now, let's talk about smaller level permissions. What about sharing one page, one folder, one part of my notebook? So, to share a page or folder, right click, select share.
Now, I could create and invite someone to just this one SOP's folder. So, let's say I'm going to invite a different email this time. Test2 at test.com. And select view or edit.
Now, when I select view, this person can view only the SOP's folder. Not the other folders, not the other pages, only things in that folder. And we'll go ahead and do that.
So, test sets up their account. You'll see a little two-person icon letting you know someone has access to just that folder. And I can go to another part of my notebook.
And select permissions. And go to the groups or people with access tab. So, these are the people who have access to this particular folder, page, or entry.
So, you see Hannah Clark, she's the owner. Test, he's a user and can edit. Test2, who we just invited to one folder, has no access to our main descripts.
Because we haven't invited them to it. And I can come in and say, you know what? Test2, he can edit this folder. Now, some groups go through the notebook this way.
They give you access to one folder, edit access to another folder, adjusting permissions, and kind of changing that out. So, you can always adjust permissions as you go. In general, I find it easy, if it's someone you work with day to day, it's someone you trust, go ahead and add them to the whole notebook.
So, you don't have to go, oh, did I give you that folder? Did I give you that page? Do you have this part? It can get a little bit confusing. And Jessica made a great point about notebook transfers. Do you want to say that? Yeah, I just wanted to mention, you know, technically, it's easy for us to move notebooks if somebody needs.
But we want to respect your privacy. And so, we require permission if it's a lab from the PI or if it's an office study from a dean. So, you know, if those people are busy, it can take weeks.
So, you want to share your notebooks in advance with the right people, so they don't lose access to important data during that time when we're trying to get the permission. Okay? Absolutely. Yeah, the sooner you can get the ownership correct, the better.
So, you don't have to deal with paperwork. Because no one wants paperwork. So, let's keep it easy.
And if you're ever concerned about, you know, notebook ownership, if you like the word notebooks, you will quickly see who owns that. So, this notebook here, it's owned by my other account, Hannah Clark, whereas these in bold are notebooks that I own. So, if I'm the PI, the ones in bold, good to go.
The ones not in bold, maybe I need to reach out to that person and have them transfer to me. Or maybe I'm not the PI. I should transfer ownership to my PI.
And we would recommend that. All right. Are there any questions on anything so far? All right.
So, the other part of this kind of session, the first one, is talking about, you know, maintaining agreements with data sharing agreements and data use agreements and all of the fun legal compliance and agreements that we make about who can access what. Now, in the academic area, we are often very flexible. Anyone can own data.
Anyone can have access to data. But in the commercial world, that is not the case. We want to make sure that kind of the least privileged possible is a good idea.
And I would absolutely recommend that practice. That means if someone is not part of a project, don't invite them. They don't need access to do their job.
They don't need to be aware of it. Don't add them. Now, if someone needs to be able to share, make them an admin.
If they don't need to be able to share, make them a user. Similarly, when people leave, you should remove their access. So, test on graduation day or not too far after it, I should click that trashcan icon.
Now, this will be taking care of you for you automatically. As people, when they graduate, within a short amount of time, their single sign-on credentials will expire naturally. But I recommend when people leave your team, when staffing changes occur, new people come on, new folks leave, make sure that this is correct.
It's just a couple of clicks, but it's helpful to make sure that you're following good practice, that your team is in communication, and you never want to risk that someone has left and had access to something that you didn't want them to have access to. So, do try to keep that in mind. Something else I will bring up, if someone ever invites you to something that you don't want in your account, which does happen, at this action column in Notebook Manager, you see this little Remove Me button. So my colleague here invited me to a corporate notebook. I am not part of that project anymore.
I may have reached out to them and said, hey, can you remove me? And they didn't, they weren't in the mood. Well, I'm gonna remove myself. I would click this button and confirm.
I would no longer have the ability to view, download, edit, or work in that notebook at all. I'm not going to, but I can. So that's something to bring up as well.
What I often recommend as part of kind of good data management practices is have this as like a five minute thing once a quarter where you just double check that all the permissions are set how you want, right? If someone joins in August or someone leaves in May or whatever else, just make sure that it's up to date and you can always ask your site administrators as well. So if you're ever worried that, hey, someone left, we think they owned notebooks, we're not sure, your site administrators can check for you if you're ever worried. So definitely recommend check ahead of time if you can.
All right, so we're running towards the end of the session. What I will bring up is another example of a slightly different kind of notebook structure. This is an example of how perhaps like an animal research lab might organize their notebook.
So they have a folder for templates, kind of pre-formatted surgical records and things like that. Then they may have related projects as a folder. So in this case, I believe it's a mouse in this case.
So we have the various cage cards and details for each mouse that we work with and all of the records for certain projects. So this is very common for like core facilities where they have much shorter term projects, right? I'm gonna do this mouse project for two weeks and then the mouse are leaving, we're getting new mice. So we're gonna start project B. So this is another very common structure for the notebook for folks like that.
Another great example of very regimented research is that corporate notebook I mentioned. So I find that especially core facilities, regimented processes, those who do very standardized research, their notebook ends up looking something like this. So I have a new projects folder where everything that's new and not assigned to someone is located.
Within the in progress folder, we have those sub folders. So I can see what's assigned to Hannah or Sherry or Linda in our team. This is really helpful if people go out of town and or someone gets called away, they had to leave early for the day, they can actually have a page and say, oh, Hannah was working on that, she left early.
Let me see if I can help out for her and kind of continue on so that she doesn't, have to throw anything out or restart or anything. Now, if you are a group that has any quality assurance or quality control, this is generally gonna be our more corporate kind of folks. So it could be those who are FDA compliant, it could be those working with patents, it could be involving page signing or page witnessing, which is a topic for the next session.
I would recommend having a quality assurance control folder because everything that's under QA is in that folder. Because when I know that, how do you go and take a look and review it? I'm gonna check that folder. If it's still in progress, I don't need to worry about it.
This is more kind of like a project management sort of thing where we sort of update the state of that page. As things complete, I move it to a completed folder. So those are all the experiments that we've completed recently.
I might organize those by date or an experimental number, a sample number, something like that, so I can quickly see what's going on. All right, so I think for the next section, we're gonna talk about, I'm reading out the topic, supporting a research data management and sharing plan and all of the kind of tools and features to support that, which is gonna be page signing and witnessing, a little more about permissions and kind of good research data practice and kind of adding data, audit trails, all that fun stuff. But I think that has everything that we had on our list of topics for this particular session.
So to start with some of the basics, I'd like to cover a couple of slides just to kind of talk about what is LabArchives. So at LabArchives, we actually have four different products. I'm going to be focusing on the first one, which is our ELN, or as Columbia First called it, an electronic research notebook used to securely store, search, and share research and scientific data.
Now, a lot of my examples today are going to come from the wet lab side of the world, because that's my personal background, but you can use it to communicate with your team about your projects. Now, we also have inventory, scheduler, and there are separate tools that are not currently part of the Columbia license, but the ELN for education has been in use at for many, many years now. It's going to be all the same tools and features we talk about today, but for course use.
So think of like a biology or chemistry based course where you have students completing assignments, that assignment is graded, and kind of that more preparing students for their future career in science side of the world. Now, what is a lab notebook? What is an electronic notebook? I like to think of LabArchives as more of a collaboration tool, right? It's for you and your colleagues to work together with your data, and our goal as a company is all about reproducibility. If I spend many years working on a project, I'm going to end up with a figure, figure four in our publication, and this publication, if someone ever looks back at it and says, hey, can you show me the data for figure four? Well, hopefully we can go back to a repository, we can go back to the supplemental data and find the related information.
But as we know, there is much more behind that work from methods, procedures, materials, equipment reservations, equipment calibrations, notes and observations, and discoveries along the way that are important intellectual property that prove that you're doing the good work that you're doing. So, I like to say it's more the story of your data, you know, everything from coming up with the idea all the way into sort of the publication of your work. If you don't have an account right now, you're welcome to make one.
Go to LabArchives.com, you'll see a single sign-on drop down where you'll log in with your Columbia credentials and get right into your notebook. Now, there are many permissions at LabArchives. The highest level role is that of the notebook owner.
Now, I would highly recommend that notebooks are owned by a central person, and more specifically, it should be whoever's responsible for that data. Usually a PI or supervisor, department head, someone who intends to be at Columbia for the sort of foreseeable future. Now, our PIs are lovely folks, they're very busy, they usually like to kind of delegate to other folks to kind of handle the day-to-day operations of the notebooks, and that's where those admin roles come in.
An admin can add data, can edit data, can invite people on behalf of that notebook owner. So, it's sort of your right-hand person. The other role there is user.
A user can add, they can edit, they can view and download. They can't share. So, they can't invite someone at NYU or Harvard or Duke or wherever.
They can simply work within the notebooks that they've been given access to. The other role there is guest. Now, guests might be undergraduate students, interns, volunteers, people outside of Columbia might be added in as a guest.
It's more for kind of short-term collaborations. And someone can have many different roles. Their roles can vary per notebook, and you can always change someone's role.
You can transfer ownership. It's very flexible on that front. Now, the talk for today, this first session, is all about notebook setup, and that really gets into the structure of your data and what makes the most sense.
Now, generally, I recommend taking a step back and looking at your work in the long term. So, if I look back at my data five, six, seven years from now, how would I find it? How would someone else find it? Would they know, oh, this is work by Hannah, so it's going to be in Hannah's notebook? Would they know, oh, this is work done in 2026, it's going to be in the 2026 notebook? Or, and I think this is more likely, would they know what project or process or, you know, trial was this part of? And that's often the most common in my experience, and that's why I generally recommend making notebooks on a project basis, right? All the related data goes into the same notebook. Now, we are always going to have data that doesn't fit into one project.
It could be procedures, policies, protocols, safety documentation, equipment maintenance policies, stuff that everyone needs, and you want to keep that documented, you want to keep that shared among the team, but it's not specific to one project. It might be the same, you know, tissue culture, fume hood is used in many different projects, but you need to keep track of the kind of maintenance of that equipment. Now, to give kind of two examples, so the left-hand side, this is a lab-wide notebook, where I have my ELN policy, maybe I have a copy of our data management and sharing plan, maybe I have our protocols, our templates, our policies, notes, weekly meetings, things like that.
Everyone can add to it, update it, it's shared across a whole group. Now, the right-hand side, I have more of a project-based notebook, where all the data related to a certain project is located. So, I might have the protocols that are relevant to that project, the samples related to that project, each of the experiments, and maybe there are different phases or goals within that project, so that it's a one-stop shop.
Everything related to that data is all together, everyone working on that project has access to it. Now, the reason I like the project-based structure, related data goes to the relevant notebook, related team members have access to the related notebook. So, let's say hypothetically our group has three notebooks, X, Y, and Z, all the related data goes to the right notebook.
If you're part of project X and Y, you're in those two notebooks. Project Z might be a little special, not everyone gets access to it, it's a little more kind of a privileged information, a more private project that not everyone's working on, so I can restrict access to that notebook. Now, very often, especially for our clinical folks, our shared services folks, our more core facility side of the world, a sequential notebook might be useful.
So, this could be a notebook per year, per business quarter, per semester, and if you have a very long-running project, lots of collaborators, lots of people working in it, the date can be helpful, right? So, I can go looking for data from 2023, it's going to be in the 2023 notebook. So, that can help if you've got very long-running work. Now, after today, if you attend all three sessions, you will be a lab archives expert, but if you have any questions after today, you are more than welcome to reach out to us.
So, of course, you have the excellent team on campus at Columbia to help answer questions, give guidance on policies, all that fun stuff, but you can also reach out to our support team. So, that would be support at labarchives.com. We also have a knowledge base, quick start guides, additional materials, and more. So, you can learn all about various tools and features.
So, I wanted to pause and see if there were any questions. We've had a lot of folks join the last couple of minutes. Welcome.
As a note, I think they mentioned earlier, the session is being recorded, and if you have any questions, you're welcome to use the chat panel. I'll keep an eye on that. There was a question, and I answered it in the chat, but maybe you wanted to discuss it a little bit.
Absolutely. So, reading this out for the room and also for the recording, the question is, is there a storage limit per user? So, and Jessica answered it, a lot of people, including Columbia, will describe the storage as unlimited, which more or less it is. I always add a big asterisk to that, because you always have, you know, the joke is, there's always someone with bigger data, because there is.
When you talk about your high performance computing folks, your large microscopy and sequencing folks, you have excellent resources. The research data team would love to chat with you about where to store that data, but for a lot of researchers, laptop crams might be all the storage you need. So, it's four gigs per individual file, so each individual attachment can be up to four gigs.
We generally recommend less than 30,000 entries per notebook, less than a terabyte per notebook, but what Jessica said is very true. We often say unlimited, because there's no limit to the number of pages, folders, notebooks, users. You can keep going as long as you need, though, you know, of course, if you start hitting a point where you have a need for high performance computing, what I usually say is, if you find that you're having to wait for your network to upload a file, and it's inconvenient for your workflow, there might be other ways.
There might be servers that are more physically located somewhere in Columbia, or broadly, maybe in New York, that are a little bit faster, that are more for your workflows. So, if you're all the big data folks, it doesn't necessarily mean you wouldn't use lab archives, it just means you'd have pointers out to the raw data, wherever that would be slurred. All right, any other questions on anything so far? All right, perfect.
All right, so let's talk about lab archives. So, what you're seeing on the screen here is a notebook. This is a notebook called Research Project ABCD.
We're going to talk about notebook setup, and creating folders, and permissions for today, or for this first session. Now, this is the notebook that I've had running for quite a while. At the top here, I have my data management and sharing plan, and the policy is from my lab on how we want the notebook to be used.
This is totally optional, but I think it's a nice way to have this information all together, because someone five years from now is going to look back at this notebook and say, wait, which grant was this part of? Who was working on this? What was the purpose of this? How were they naming those files? So, it's nice to have this sort of thing in a centrally shared place. Now, this notebook is more what I would call a workflow-based notebook. So, my group has lots of page templates that are preformatted, and anything in the in progress folder is in progress.
We're working on it currently, whereas things put into the completed folder are completed. So, I can really quickly see what's going on within my group, who's assigned to what. Maybe I have additional subfolders for each person in my group.
So, if the page is in in progress and in Hannah's folder, that means Hannah's working on it right now. So, the pages can obviously be moved, and copied, and updated as well. Ultimately, data is added to a page.
So, this is my page for Experiment 101. At the top here, I have the notes and steps for Experiment 101. It could be a procedure.
It could be observations. I might have materials as part of my experiment. And down here, I have some files.
Now, as mentioned, we can upload files of any file type, whether that's something we integrate with, like GraphPad and Snapseed, or things like images, office documents, PDFs, and even more proprietary file formats. So, if you have a unique piece of software for the equipment and tools you have, excellent. That data can certainly go into LabArchives.
Now, you'll notice on every entry, there's tools for working with these entries, and I'm going to talk about these more in a second. On the right-hand side, you see a date and time stamp. Now, when we talk about LabArchives, this is kind of the reason you would use LabArchives.
It gives you the ability to see exactly what was done, who did the work, what changes they made. You can review every single version of an entry. You can revert to earlier versions.
You can review them. You can undelete them if you need to. You have a full record of what was done, who did the work, when they did the work, and you can always go back and prove that you're doing the good work you're doing.
So, that's what you need. Now, I'm going to go and talk a little bit about how to make a notebook, how to establish some folders, and how to invite your colleagues. Before I do that, are there any questions so far? All right, let's see.
All right. So, at the word notebooks, you're going to see all the notebooks that you have access to. And in that you all are part of Columbia, there's a notebook that I don't have that you will, which is a site-wide notebook owned by the Columbia team that has some documentation for compliance and IRB and all that fun stuff.
So, do take a look at that. It's a great resource. So, that's going to be your read-only notebook you're going to see in the list.
At the plus icon here, you can make a new notebook. Now, we talked about before you might make a notebook for each project, each grant, each workflow with your team. So, let's say our team has a brand new funding for project Z. I'm going to make the project Z notebook.
Now, a lot of people want to start from scratch. I want a blank notebook with no folders. So, they'll pick that no option.
Some people like the project structure. So, to see what that would look like, the project structure gives me these folders here for protocols, a sample log, experimental data. If I use that lab-wide structure, it gives me more of what a lab-wide notebook might have.
Is there content within those folders, or are they empty? Yes. The question is, is there content in those folders? The folders are totally blank. It's just a couple of empty folders for you to kind of get an idea of what's possible.
Now, so, no pages, no entries, just a couple folders. Now, when I click create and confirm, I have a new notebook that I own. So, at the word notebooks, now you see I have four.
Now, if your group has been using lab archives for a while, you might go, hey, I have 30 notebooks. I'm not accessing the ones from 10 years ago. You can actually hide notebooks.
It's the option right here. We call it our notebook manager. So, you actually see I have a couple of hidden notebooks already.
These are things I don't go to as often, and you can unclick that included navigator so you still have them, still get to them. You just don't have to see them day to day, which is sometimes nice for groups who have lots of notebooks. The other thing to point out here is the clone button.
So, these are over here on the right-hand side, this little two squares button. This is going to create a full copy of everything. So, let's say the question before, I have some pages, folders, content, ready to go.
I want two of these notebooks that look the exact same. You can clone them. The nice thing about cloning, it copies everything in the notebook, all entries, all pages, all folders, and all permissions.
So, if your group has already been set up and going, you have a notebook that you like, you can clone it and put new data in for a new project, perhaps. Now, our project Z notebook, you see we have a couple of folders here for protocols, a sample log, and if you right click, you've got a lot of options with folders. So, you can add a new subfolder in there.
You can copy from this notebook or from another notebook. You can even rename. So, maybe I don't want this to be a sample log.
I want this to be SOPs, Standard Operating Procedures and Safety Documentation. Then click okay. So, now the folder is called SOPs and Safety Documentations.
Similarly, I can move folders around just by dragging and drop and even move them within another folder as kind of a subfolder there. Now, the folder structure is totally customizable to what you want to do, and I always recommend to groups to have a conversation with your team about what makes sense for your projects and for your notebooks. If you're joining a lab that's already been used in lab archives, the folder structure might be established, but you can always change it around.
So, if you jump in, you get started, you set up your notebooks, and then you go, I don't like this. I want to change it. You can.
You can rename things. You can move it around. Add new folders, new pages.
It's very flexible on that front. You can rename. You do see an option to delete.
Now, keep in mind, no entries, pages, or folders are ever permanently deleted. So, let's say I delete my references here. I don't see them on the main list of folders.
However, they're just right here in our deleted items bucket where I could always unbleed and bring it right back in the book. So, just keep that in mind. Nothing is ever permanently deleted.
Once it's in your notebook, it's part of that record from today forward. Now, I want to hop into talking a little bit about permissions before we talk a little bit about kind of adding some data to a notebook. I don't see any questions so far.
So, keep going. All right. So, in order to kind of set up a whole labs notebooks, I might repeat this process a handful of times.
I might make five, six, seven notebooks if I want to, or I might just start with one. Now, I can manage access at the notebook level, at the folder level, at the page level. Most of the time, access is at the notebook level, and that's generally what I would recommend.
To manage access for notebooks that you own, click your name and go down to account manager. Now, this shows the people in my group and the notebooks they have access to. So, if I have someone new, click the add person icon and type in their email.
Now, it's worth ringing up at Columbia. It seems like some of you all have many, many, many formats of your email. You can invite someone with whichever email address they prefer.
So, if it's a particular format, make sure that's the one you invite them with. If it's someone outside of Columbia, you can invite them as well. Obviously, make sure that's in line with compliance and the data use agreements that you have, but you can type in their email and pick their role.
So, I talked briefly about roles earlier, but I didn't explain the difference between account admin and notebook admin. So, an account admin is your right-hand person. They can add, they can edit, they can share everything in my account.
Every notebook that I own, they can make more notebooks for me. That is a person I trust with everything. Now, sometimes, maybe they're not responsible for everything.
Maybe they're just responsible for some of the projects. Maybe just project Z. Maybe just project ABC. Maybe both of them.
And you can pick. And it might be the case where they're an admin in one notebook or a user in another, right? They're not allowed to share our data management policies. Most people in your group, most lab techs, grad students, med students, researchers in your group will have the role of user.
They can add, they can edit, they can work. They can't share. So, they can't invite their friend down the hall.
They can't go invite someone at another institution. They can simply work within their data. Now, you'll notice I can also give you only access.
So, some groups do make a notebook per person, right? So, the Clark Lab has a notebook for Jim, Jill, and Johnny. Jim, he gets edit access to his own notebook, but you have access to Jill and Johnny's notebook. So, you can choose to kind of set that up as you see fit.
The last role there is guest. We do highlight there 60 days of editing access. This person would be invited with temporary editing access for just about two months to those two notebooks.
So, something to keep in mind. Now, I'm going to add test here as a user to these two notebooks and confirm. When you invite someone, if they don't have an account, they'll get an email saying, hey, you've been invited to an account.
Click on this link to make your account. They'll log in and have access to your notebook. If test was previously using LabArchives, they already have an account.
They would just log in and get access. As a little pro tip, whenever you invite someone, if they already have an account, you're going to see their first and last name listed. So, there you see Clark Hannah.
That's an activated account. She has set up that account. She's logged in.
Test here hasn't logged in yet. So, we know that because we don't see a first and last name. The reason I bring that up, if you ever do invite someone with the wrong format of their email, that can be a nice quick sign to say, oh, yep, wrong format.
Now, at any point, I can change someone's role. So, I can make them an admin, a user, a guest. And I can also remove someone's access.
So, test, ah, he's been the best graduate student in our group. We're very sad. He's graduating.
We're happy for him. But sad for us. Let's go ahead and remove his access.
Trash can icon confirmed. This removes their access to all notebooks that I own. Now, let's say they're leaving our group, but they're still at Columbia.
That's great. They can go work on their other notebooks with their new lab or maybe their new PI and setting up their own notebooks. They can do that.
If someone is leaving your institution, obviously, make sure their access is updated. But you can also click the notebook icon to see which notebooks they have access to. So, my other account here is a notebook admin and just one of my notebooks.
Now, most PIs, most supervisors, account managers is how they manage access. It's real quick. One click, add someone to several notebooks.
Some groups want to manage access on a smaller basis. So, maybe I want to share just our brand new notebook here. Project Z. Triple dot menu, go down to notebook settings.
There are some settings you can adjust. I'll talk more about page signing and witnessing later on. Under user management, here are the people who currently have access to our Project Z notebook.
If I want to add someone new, click new user and invite them. So, I'm going to go back. Test, we're so excited he's returned.
So, we're going to invite them to this one notebook and confirm. So, Test is back. He has access to this one notebook.
He does not have access to the other notebooks in my account, just that one. And again, I can adjust his role to this one notebook if I want to. Now, an important thing to point out is this button right here.
Ownership transfer. So, as you mentioned at the very start, notebook owner is the highest role. Generally, that should be PIs, supervisors, managers.
And very often, PIs like to delegate the responsibility of setting up the notebooks to someone else. Maybe it's yourself, and that's why you're on the call. Welcome.
We're happy to have you. Feel free. Make your notebook, set things up.
Within a couple days, a couple weeks, I recommend transferring ownership to the PI or at least to a central person. Because sometimes we have grad students who go in and make a bunch of notebooks, add a whole bunch of data, all working great. They graduate, they move on, and they forgot they still own that notebook.
And that happens. It's no big deal. We can take care of it.
Reach out to your site administrators. It's like three clicks to fix. But I recommend just to take something off your plate for graduation day, go ahead and transfer ownership.
And no matter what, no matter whether you use web archives or other tools, I would always recommend that your PI has access to your data. Whether they use it, whether they look in and take a look is up to them. But definitely make sure they at least have access to your work and know where it's being stored.
Because they should. Now, let's talk about smaller level permissions. What about sharing one page, one folder, one part of my notebook? So, to share a page or folder, right click, select share.
Now, I could create and invite someone to just this one SOP's folder. So, let's say I'm going to invite a different email this time. Test2 at test.com. And select view or edit.
Now, when I select view, this person can view only the SOP's folder. Not the other folders, not the other pages, only things in that folder. And we'll go ahead and do that.
So, test sets up their account. You'll see a little two-person icon letting you know someone has access to just that folder. And I can go to another part of my notebook.
And select permissions. And go to the groups or people with access tab. So, these are the people who have access to this particular folder, page, or entry.
So, you see Hannah Clark, she's the owner. Test, he's a user and can edit. Test2, who we just invited to one folder, has no access to our main descripts.
Because we haven't invited them to it. And I can come in and say, you know what? Test2, he can edit this folder. Now, some groups go through the notebook this way.
They give you access to one folder, edit access to another folder, adjusting permissions, and kind of changing that out. So, you can always adjust permissions as you go. In general, I find it easy, if it's someone you work with day to day, it's someone you trust, go ahead and add them to the whole notebook.
So, you don't have to go, oh, did I give you that folder? Did I give you that page? Do you have this part? It can get a little bit confusing. And Jessica made a great point about notebook transfers. Do you want to say that? Yeah, I just wanted to mention, you know, technically, it's easy for us to move notebooks if somebody needs.
But we want to respect your privacy. And so, we require permission if it's a lab from the PI or if it's an office study from a dean. So, you know, if those people are busy, it can take weeks.
So, you want to share your notebooks in advance with the right people, so they don't lose access to important data during that time when we're trying to get the permission. Okay? Absolutely. Yeah, the sooner you can get the ownership correct, the better.
So, you don't have to deal with paperwork. Because no one wants paperwork. So, let's keep it easy.
And if you're ever concerned about, you know, notebook ownership, if you like the word notebooks, you will quickly see who owns that. So, this notebook here, it's owned by my other account, Hannah Clark, whereas these in bold are notebooks that I own. So, if I'm the PI, the ones in bold, good to go.
The ones not in bold, maybe I need to reach out to that person and have them transfer to me. Or maybe I'm not the PI. I should transfer ownership to my PI.
And we would recommend that. All right. Are there any questions on anything so far? All right.
So, the other part of this kind of session, the first one, is talking about, you know, maintaining agreements with data sharing agreements and data use agreements and all of the fun legal compliance and agreements that we make about who can access what. Now, in the academic area, we are often very flexible. Anyone can own data.
Anyone can have access to data. But in the commercial world, that is not the case. We want to make sure that kind of the least privileged possible is a good idea.
And I would absolutely recommend that practice. That means if someone is not part of a project, don't invite them. They don't need access to do their job.
They don't need to be aware of it. Don't add them. Now, if someone needs to be able to share, make them an admin.
If they don't need to be able to share, make them a user. Similarly, when people leave, you should remove their access. So, test on graduation day or not too far after it, I should click that trashcan icon.
Now, this will be taking care of you for you automatically. As people, when they graduate, within a short amount of time, their single sign-on credentials will expire naturally. But I recommend when people leave your team, when staffing changes occur, new people come on, new folks leave, make sure that this is correct.
It's just a couple of clicks, but it's helpful to make sure that you're following good practice, that your team is in communication, and you never want to risk that someone has left and had access to something that you didn't want them to have access to. So, do try to keep that in mind. Something else I will bring up, if someone ever invites you to something that you don't want in your account, which does happen, at this action column in Notebook Manager, you see this little Remove Me button. So my colleague here invited me to a corporate notebook. I am not part of that project anymore.
I may have reached out to them and said, hey, can you remove me? And they didn't, they weren't in the mood. Well, I'm gonna remove myself. I would click this button and confirm.
I would no longer have the ability to view, download, edit, or work in that notebook at all. I'm not going to, but I can. So that's something to bring up as well.
What I often recommend as part of kind of good data management practices is have this as like a five minute thing once a quarter where you just double check that all the permissions are set how you want, right? If someone joins in August or someone leaves in May or whatever else, just make sure that it's up to date and you can always ask your site administrators as well. So if you're ever worried that, hey, someone left, we think they owned notebooks, we're not sure, your site administrators can check for you if you're ever worried. So definitely recommend check ahead of time if you can.
All right, so we're running towards the end of the session. What I will bring up is another example of a slightly different kind of notebook structure. This is an example of how perhaps like an animal research lab might organize their notebook.
So they have a folder for templates, kind of pre-formatted surgical records and things like that. Then they may have related projects as a folder. So in this case, I believe it's a mouse in this case.
So we have the various cage cards and details for each mouse that we work with and all of the records for certain projects. So this is very common for like core facilities where they have much shorter term projects, right? I'm gonna do this mouse project for two weeks and then the mouse are leaving, we're getting new mice. So we're gonna start project B. So this is another very common structure for the notebook for folks like that.
Another great example of very regimented research is that corporate notebook I mentioned. So I find that especially core facilities, regimented processes, those who do very standardized research, their notebook ends up looking something like this. So I have a new projects folder where everything that's new and not assigned to someone is located.
Within the in progress folder, we have those sub folders. So I can see what's assigned to Hannah or Sherry or Linda in our team. This is really helpful if people go out of town and or someone gets called away, they had to leave early for the day, they can actually have a page and say, oh, Hannah was working on that, she left early.
Let me see if I can help out for her and kind of continue on so that she doesn't, have to throw anything out or restart or anything. Now, if you are a group that has any quality assurance or quality control, this is generally gonna be our more corporate kind of folks. So it could be those who are FDA compliant, it could be those working with patents, it could be involving page signing or page witnessing, which is a topic for the next session.
I would recommend having a quality assurance control folder because everything that's under QA is in that folder. Because when I know that, how do you go and take a look and review it? I'm gonna check that folder. If it's still in progress, I don't need to worry about it.
This is more kind of like a project management sort of thing where we sort of update the state of that page. As things complete, I move it to a completed folder. So those are all the experiments that we've completed recently.
I might organize those by date or an experimental number, a sample number, something like that, so I can quickly see what's going on. All right, so I think for the next section, we're gonna talk about, I'm reading out the topic, supporting a research data management and sharing plan and all of the kind of tools and features to support that, which is gonna be page signing and witnessing, a little more about permissions and kind of good research data practice and kind of adding data, audit trails, all that fun stuff. But I think that has everything that we had on our list of topics for this particular session.