CERF Electronic Lab Notebook (ELN)

CERF Electronic Lab Notebook (ELN)

Welcome to CERF the electronic lab
notebook. CERF is 21 CFR 11 compliant. This is a government requirement for
record retention this means that your records can’t be tampered with or
falsified. Anything you delete is still recorded and saved in the system so you
can always go back and see the full audit trail. The CERF server runs with an
Apache Tomcat and uses additional third-party tools such as the OpenOffice
engine to provide an array of functionality to your workflows. It can
run physically or in a virtual environment, locally or on a cloud
deployment. Once you have your CERF server installed there are two ways that
you can access it: one is through the web client using your web browser and the
other by using the full featured desktop app. Let’s take a look at the web client
first. I’m using Safari here. When you log in as a standard user, you have access to
basic tasks like password management, notifications, as well as bookmarks and
your own personal work group management. If an admin user logs into the same
place, you can see they have access to more features. First and foremost here on
the dashboard you can see that everything is working. You can check on
your OpenOffice engine, you can view your administration and your license. On the
left you can access work group management, signature group management,
and user management. You can view all the system resources, you can view all the
file cabinets, and all the notebooks for your whole deployment. Everything is
listed here for the admin. You can search for specific data and again this search
is the whole system you can import and export data if you need to back up your
system or migrate to a new surf server just select it and choose the export
button here at the bottom you can browse to any resource at any time and export
that way the data is stored as XML bundles by default which are great for
archiving if you’re making a backup of something to save it for later we also
have a standalone export manager that allows conversion of these bundles to
human readable data you can view your logs and reports and your settings if
you’re an admin you can come in here and see exactly how your server is being
used you also have access as an administrator
here business policies these allow you to tweak the behavior of your server to
match your organization’s policies and sops here you’ll see password policies
you can allow or disallow different types of editing you can choose your max
size for file upload virtually the entire system is configurable from this
page as you describe your workflow to us we can help you come up with ways to
tweak these settings to match exactly what you are already doing that way
there’s no learning curve and you don’t have to change anything when you start
using surf the main way that the users will be accessing the system is with the
full featured desktop client which I have loaded up here this is available
for both Mac and Windows it’s written in Java so it looks exactly the same on
either platform go to login and here you can see you can connect to several
different bookmark servers it gives you the status of each whether it is up and
active or turned off and not accessible right now you can change those bookmarks
here by clicking edit servers here you can add new servers or you can edit ones
you already have I’m going to connect to our main server that we use for our
documentation but I’m just going to be showing you demo resources on that
server I’m logging in as a standard user anytime your server is updated your
client will automatically download and install updates from the server so you
won’t have to go around to every workstation and update the install there
nor will they have to run any kind of updater to make that happen it happens
automatically simply by logging in whenever your server is updated or when
we release a new build or updated components after logging in you’ll see
that there are two sides of this desktop client that can function totally
independently of each other as you’re working on the right side you have your
inbox used to get data into serve by sending emails you can view attachments
and drag them straight into your file cabinets controlled documents used to
set up specific documents that can only be used by specific people you can view
the people and you can set reminders for signing next we have the notebook pain
this pane shows whichever notebook is currently loaded from the left-hand tree
after that notifications where you can find notifications for just about any
data and forms where you can set up samples that are reusable and we can
help you configure custom data types to enter for your own organization and
search surf has a powerful leucine based flexible search engine you can search
for anything and you can build filtered elaborate searches that make it easy to
find anything you need and you can even save those searches to come back to them
later at the top of the left hand side you’ll find the documents pane this is
also referred to as the surf tree it shows the documents that you’re
currently working with you can show more or less of the files that you have
access to at any time just go to collections show collections the left
list shows what I’m currently viewing in my tree and the right pane is everything
that I could be viewing if I wanted to display it I can change this and add or
remove at any time the next pain is for checked out documents any document
you’re editing will show up here and other users will be able to see that
they cannot edit the file while you are editing it here you can easily see what
you have checked out check things back in or if you want to cancel your changes
you can uncheck out here are your bookmarks the bookmarks you can organize
and sort within folders you can add a bookmark to anything in the system here
we have all of your saved searches and the last one the hard drive is your
local files this is the computer that you were working on so if you need to
load something into surf from your desktop you can do it here if you want
to save something from surf to your desktop you’ll do that here also and
you’ll notice that as I click the icons on the right the pain switches back and
forth between the different sections that you’ve selected but what’s nice
about surf is that on the left hand side the pains will stack up for you you can
close any single pane you like if you just want to view a single one or you
can add more in to make it more convenient for you that way you can
easily access multiple things at once and still see the notebook that you’re
working in on the right hand side so let’s focus in on the documents pane or
surf tree this pain is made up of what are called collections there are two
types of collections file cabinets and notebooks file cabinets are these brown
icons they are analogous to your hard drive on your computer
except this is stored within surf so it’s secure encrypted and regularly
backed up as well so you don’t have to worry about anyone keeping files on
their own computer that could crash letting them into a file cabinet retains
them forever it’s easy to make new collections just click the plus icon and
choose new notebook notebook collection or file cabinet and once you have one of
those within them you can create a new folder or add a resource from the menu I
can choose a signature workflow and I can create an empty or from a template
will talk about templates in a minute I just click create and immediately you
can see my new file cabinet displayed in my tree to import documents you can drag
and drop or use the local files pain down here the system will show you the
progress of the upload and when the upload is complete you can see that my
whole folder hierarchy is retained when you right-click items to view a
read-only copy is downloaded and surf automatically knows which application is
correct to view this document since it’s in a read-only state other users can
make edits to it if they need to if you want to make edits just double-click the
file or choose edit check out an edit from the right-click menu when you check
out a file for editing the system puts a checkmark next to the icon for the file
that checkmark displays for everyone so at a glance people can know that the
document is currently being worked on they can still view the document but
they will not be able to make edits until you check the file back in after I
make my edits I can choose save and close and then in my checked out
documents pane select it and choose check in that updates the document with
my latest changes right clicking on the document you can view the resource info
this allows you to view all of the metadata associated with that file as
well as the version history so as you make edits to the document all previous
edits of the document are retained so you can go back in time you can see what
was done and who changed it the metadata is also searchable so as you’re in the
search window you can search for specific metadata that you know is in
there the contributor or a version number or even the date and load up
everything that matches now let’s take a look at note books
notebooks allow you to tell the story of your research they are divided into
sections and pages either of which can be loaded from templates I’m going to
select a page here and click the I button to view it on each page you can
see that there are entries one after the other entries function the same way
everything else does they have versions and metadata associated with them when
you select an entry you see the checkout neta buttons delete view info edit
metadata you can add notes strikeout even finalized entries if we just wanted
to edit this you can double click on it or choose check out and edit adding
entries is easy to get started you can double click on the page this loads the
text editor everything you’re familiar with a microsoft word bold italicize
underline changing fonts font size links copy paste you’ll find here but if you
don’t like the text editor maybe you’re more accustomed to using word that’s
fine too because you can drag and drop files right to your notebook page so if
you’d prefer to record your day in your own text editor you can save the file
and drag it to your notebook page you can drag and drop directly from your
desktop or from a file cabinet surf allows you to view text documents
spreadsheets presentations PDFs all image types trace files from sequence
machines mind maps sketches all auto rendered in line on your notebook page
and you can check them out and edit them just by double-clicking them you can
insert structured documents from your sample collection so that you can link
directly to samples you are using that day you can add audio recordings if
perhaps your hands are gloved or your otherwise unable to type you can create
a simple recording as an entry on your notebook page surf’s pages also support
inline viewing of molecule and chemical files stir friend errs the chemical
structures in line these are not previews these are the actual content of
the files you can even rotate the files to get a good idea of what’s going on in
the chemical bonds surf even includes a built-in table tool that looks and
functions like an Excel document you can take items already in surf like your
protocol and drop it into a table cell by doing that you can
elaborate workflows with sample specifications results and with the
ability to sign in a particular cell you can have multiple co-signers it can
perform math functions and you can even use it to represent gels one of the best
features surf has is the ability to add any file type to your collection if surf
receives an unrecognized file it treats it exactly like all the others and
allows you to check out edit version just like anything else if the file
can’t be displayed in line you can create what’s called an official print
copy this is when you take an image PDF or screenshot of the contents of that
file from whatever application is required to view it and then set it as a
badge over top of the file in your notebook that way you can still see what
the file is just by glancing at your page and when you print your page to PDF
it will print that official print copy that you’ve overlaid on top of your file
that way you won’t just see a file name you can also add notes captions links
tags and custom metadata to files all of which is searchable you can view the
metadata here and get an idea for the different kinds of things you can search
for the metadata for all files is completely customizable when adding
files to serve the system reads everything that’s already on the file in
adds it to the search index for example if you were to upload an image from your
smartphone surf will be able to tell you what resolution it is where you took it
when you took it and so on if there’s not enough metadata by default you can
add your own so that the item is more searchable now let’s say this workflow
is the workflow you’re going to take every day for the next two weeks well
instead of rebuilding this whole page every day you can create a template from
it just right click your page and go to tools create template you can customize
the template as you are creating it by unchecking sections you don’t want to
include give it a name and then just click create template now when you
create a new page you’ll see your template available you can even create a
template from a page full of placeholders leaving spots open for
fresh data each day templates can be created not just from a notebook page
but from a whole file cabinet notebook a single entry you can make a
template from anything this video demonstrates just a subset of search
features if you are interested in a personalized demonstration or purchasing
your own surf server visit our website or send us an email thanks for watching
and be sure to LIKE and subscribe for more surf resources

Daniel Ostrander

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1 thought on “CERF Electronic Lab Notebook (ELN)

  1. Rob Day says:

    Learn more about CERF and other scientific data management products at lab-ally.com.

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