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How to evaluate the electronic lab notebook eCAT in 6 easy steps

Posted by Rory on November 22nd, 2010 @ 11:08 am

Over on the Electronic lab notebook blog I’ve just written a general post on how to evaluate software, with a particular focus on electronic lab notebooks.  In this post I’m going to guide you through the process of evaluating eCAT.

Step 1:  Poke around the Axiope website

Spend some time on the Axiope website.  You can learn a lot from the website about both eCAT and Axiope.  We try to be as transparent as possible — the website explains how much eCAT costs,  that there is a  free Personal version, and what the differences between the Personal version and the two group versions — Install and Team Hosted — are.  The website goes through what eCAT does — with videos and text that focus on the practicalities of setting up and using the software.  In addition, you can get a perspective on how other people are using it, and what they like about it, from the Who uses eCAT section.  From all  this you should be able to get a decent feel for whether eCAT looks as if it will be able to solve your problem.

Step 2:  Decide which version of eCAT to try

There are three versions of eCAT.  The free Personal version is for individual use. It’s for individual scientists who want a better way of recording and organizing research data, and value the ability to put structure into the record they keep of their research.  The other two versions, Install and Team Hosted, are for labs.   The Install version is installed on your computers behind your firewall, and it has a big advantage — your files can be ‘mapped’ to eCAT so that eCAT can see them and and there is no need to upload files.  The Team Hosted version is hosted by Axiope.  You still get administratrive control, but you don’t have to worry about computers or backup, we take care of that.  It’s useful for labs that don’t have a computer system available to install eCAT on or aren’t confident about their IT support.

Step 3:  Sign up for a trial

Once you’ve decided which version you want, you can sign up for your free Personal account and/or for a free trial of the Team Hosted or Install versions.  Some people sign up for a Personal account and get a free trial of one of the group versions.   Signing up for a Personal account or a Team Hosted trial is very straightforward — after you register Axiope sends your login details, and you can login and get started.  The Install version works a bit differently.  After you register you are taken to instructions for downloading and installing eCAT.  But again, once eCAT has been installed, you are ready to begin testing.

Step 4:  Set up testing accounts

With both the Team Hosted and Install versions, at an early stage you will want to login as the admin user and use the administrative privileges the admin user has to set up accounts for others in your group who will be testing eCAT.  That’s descibed here for Install.  For Team Hosted, logged in as the admin user, you will need to set up attachment stores for the other user accounts you set up.   You need to first create the user’s account, then save their information, and then go back into the user and edit it again to create the attachment store.   Each user will need to set up a store folder to access their files with the attachment store that has been set up for them.  The instructions for that are here.  There is also a video on how to organize your lab with eCAT, which might be worth watching before you get started setting up user accounts.

Step 5:  Try it out!

If you are a Personal user, you will have skipped Step 4, and you can just  login and get your teeth into eCAT.  Individual testers of the Team Hosted and Install versions can do the same once the person acting as admin has set up their accounts.  There is also a Getting Started video that many people find useful.

As you put eCAT through its paces there are a couple of things to remember.  First, you need to keep the problem you are hoping eCAT will solve in the back of your mind and ask yourself periodically how good eCAT is at solving the problem.  But at the same time it’s a good idea to keep something of an open mind, because using  eCAT may put the problem in a  different perspective, or even bring you to the realization that you have a  different problem than you thought you did at the outset and/or that eCAT is really useful even though it only partially solves your original problem.

Second, how good is Axiope at explaining how to use eCAT?  Are the how to videos and video interviews with users informative?  How about the brief videos inside eCAT explaining how to do certain things and perform certain tasks?  And how about the User Guide? Is it easy to navigate?  To the point?

Step 6:  When in doubt, ask

As you go through the testing, there are bound to be some things you don’t understand and for which there does not appear to be a ready explanation in the User Guide, the website, or the videos embedded in eCAT.  When this happens, don’t hesitate to ask  us by sending an email to support@axiope.com   And judge us by our response.  How long does it take us to respond?  Is our answer responsive to your question?  Is it honest?  Helpful?

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How to install and run lab software in a university environment

Posted by Rory on November 1st, 2010 @ 10:15 am

Managed IT environments

If you’re working in a university the odds are you’re in a ‘managed’ IT environment.  In other words, the computer your university supplies you with is controlled by an administrator.  That matters if you want todownload web-based  software for you or your lab to test.  It matters because you may not be able to download a test version of the software without assistance from your administrator, and once you  have downloaded the software, you may not be able to let other members of the lab access the software without administrative privileges, which you probably do not have.  This post looks at how to work within these constraints and find ways for you and other members of the lab to access software you want to test.

Servers

If you want to just test the software yourself, then you can download it onto your own computer — no need to deal with the managed computer system of your group or institution.  But if the software is going to be used by others, and you want them to be able to test it as well, you need to install the trial version of the software on a machine they can all access as a group.  To enable that you install one copy of the software on a single’ server’ machine and then use web browsers to connect to the software.

A server is normally a machine in your lab  dedicated to running services – always turned on and always connected to the lab network. The machine needs to be connected to the lab network and to allow connections to be made to it across your lab network. If you wish to be able to access the software remotely, then the server also needs to allow connections externally, which may require some configuration of your firewall. If you don’t know what the firewall allows, you may need to speak to your IT people.

Administrative privileges

Because web-based software systems are server applications that must be running 24/7,they require administrative priviliges for both the user installing the software and the user running the software. If you do not have administrative permission on your lab’s server, you will need to speak to IT to get the software installed and to run the software. Note that if you shut down the software you will need administrative privileges to start it again.

What to remember

So the key things to remember if you are testing software that various members of a group need to access as a group are:

  1. The software needs to be installed on a server.
  2. Administrative privileges are needed for both the person installing the software and the person running the software.
  3. It’s probably a good idea to speak with your IT people before you get started.

Installing eCAT

These points apply to eCAT, and are explained step by step during the eCAT trial install process.   There  is a more detailed explanation with additional background in the Support section of the Axiope website.

How to set up a new lab with an electronic lab notebook

Posted by Rory on October 4th, 2010 @ 9:44 am

I recently  came across a great primer on how to set up and run a new lab.  It’s called How to set up a new life science lab without HHMI funding, and it was put together by some people at Dartmouth to welcome new faculty members.  Their recommendations are simple:

  • You’re the best postdoc you’ll have for many years; stay at the bench
  • Grow slowly and selectively
  • Hire a research associate who is a stable person and not too proud to help you be more productive
  • Submit grants early
  • Compartmentalize and plan your time
  • Balance novel and risky experiments with meat and potatoes
  • Attend just one meeting a year

Hmm, I thought, eCAT can help with each of those recommendations.  Here’s how.

Stay at the bench

Spending time at the bench is one thing when your main focus is your own research, quite another when you have all the responsibilities and commitments that come with setting up and running a lab.  To make time for research, you’ll need to be well organized and efficient in carrying out and  documenting your experiments.  And you’ll need to be in close touch with the research  everyone else in the lab is doing — you’re not on your own or supervising one or two people any longer, you’re leading a group.

An electronic lab notebook can help on both accounts.  Larry Gonzalez  at the University of Okhlahoma summarized nicely how eCAT helps both him and his lab get better organized:

“eCAT  helps keep me organized, and it’s very good at increasing my efficiency in documenting my research.  Myself or a research technician or a post doctoral fellow can generate a protocol and store it in eCAT.  We can create the data forms that can be filled out manually and entered during an experiment, and we can link to external files.  And if someone would prefer to use another program like Excel to generate spreadsheets instead of entering data into eCAT they can create a spreadsheet and we can link to that file, and its all kept together and organized well in eCAT.  And then when an experiment is completed we’re able to export the data to an external statistical data program for subsequent analysis.”

Grow slowly and selectively

An important benefit of a good electronic lab notebook is that it is flexible enough to grow as your lab grows.  In the most obvious way, it should be able to accomodate the addition of new lab members by making it easy to set up new accounts for them.  There are also less obvious things a good ELN can help with, like  having the ability to set up groups of users.   In eCAT you can set up an  ‘all users’ group, with permissions set on what records the members of the lab can view, what records they can edit, etc.  So you don’t have to set up a new permissions regime for each new person who comes into the lab; you just add them to the all users group and it happens automatically.

Another aspect of eCAT’s ability to help integrate new lab members easily is that, as Alex Swarbrick of the Garvan Institute in Sydney pointed out,

“Since everyone uses the same interface, it is easier for new people to understand the way the lab works and to pick up on projects.”

Hire a research associate to help you be more productive

Postdocs have to be self sufficient and multi-talented to survive, much less thrive, so working with someone else who helps manage you and your new lab may take some getting used to.  To develop a good relationship with a research associate and get the most out of them involves not only interpersonal skills; you also need to establish an environment where collaboration and communication takes place as naturally and as easily as possible.

Introducing an electronic lab notebook as the place where everyone in the lab documents and shares experimental data, as well as meeting notes, protocols and other information not only makes your life easier, it also makes your research associate’s life easier.  And that’s crucial because given the explosion in demands on your time that come with runnning your own lab, your productivity is now impacted by your research associate’s productivity.  If they are left to chase bits of information scattered around other people’s paper lab notebooks, in random disk drives, and on personal computers, a lot of their time is going to be wasted.

With an electronic lab notebook, your research associate can have access to all group records, and can set up structures for recording and organizing things like lab protocols that make it easy for them, and you, to find information.  Heather McClafferty, research associate to Mike Shipton at The University of Edinburgh’s Centre for Integrative Physiology, said after the lab had adopted eCAT:

“Having everything tied together under one resource, so results, protocols, constructs, where things are physically, having everything together under one system has just been perfect.”

Submit grants early

Submitting grants early requires organization.  That’s pretty obvious.  What may be less obvious is that organization becomes a bigger challenge, but can also bring bigger rewards, when you are at the head of a group, even a small one like your first lab.  Your research associate and your students can both be useful resources for preparing for grants:  carrying out preliminary research, finding data from previous projects, and researching and preparing applications.  They will do all this much more effectively with an electronic lab notebook.  With an ELN it is easier to share data and communicate about it, data from previous projects is archived and easily searchable, and when it comes time to prepare the application, (a) people are already working in the same integrated environment, and (b) the data needed to support the application is readily available for inclusion into it.

Compartmentalize and plan your time

The organization theme is obviously relevant here.  But how does an electronic lab notebook help?  First, an online ELN like eCAT is accessible 24/7 from any computer with a web browser.  That means you don’t have to set up a specific time to see what others in the lab have been doing.  No need to make an appointment to go over a student’s paper lab book.  Instead, as Alex Swarbrick says, “I can use eCAT to remind myself of recent experimental results without hassling someone in the lab.”  And Alex, and other eCAT users, are free to arrange their time in the way that suits them, rather than having to fit in with arbitrary schedules, or what’s convenient for others.  The result is more time to spend, and to allocate in the way you find most effective.

Balance novel and risky experiments with meat and potatoes

One of the benefits of a flexible ELN is that it allows you to structure your experiments, and those of others in the lab, in the way that best suits your research.  Mike Shipston at Edinburgh put it this way:

“The great thing about eCAT is it’s incredibly flexible in terms of how you can set it up.  For example each member of the lab has their own folders and puts their own experiments within that, but its every easy to put that information together.”

Having a structured record of your lab’s experiments — yours but also everyone elses — means that you are more likely to spot patterns, discrepancies, and problems.  And see the woods from the trees and develop a better sense of what’s risky and what’s meat and potatoes, and why.

Attend just one meeting a year

This is one bit of advice you almost certainly are not going to follow!  The reality is that you’re going to find yourself on the road quite a lot, whether it’s attending a conference or meeting collaborators about a grant proposal or work on a grant in progress.  With an online ELN like eCAT, you can stay in touch with the work that’s going on back in the lab because you can login over the internet and see what people having been doing, in the evening, between meetings, or whenever it suits you.  And with eCAT’s notifications system, you can send and receive messages about people’s research, and even put links to experiments and other records in the messages, which makes it easy to work collaboratively even when you’re on the other side of the world.  So if don’t follow this last bit of advice, and end up attending meetings regularly, with eCAT you will still be able to keep up with other aspects of your lab’s research.

How to organize your lab with the electronic lab notebook eCAT

Posted by Rory on September 20th, 2010 @ 10:09 am

Background:  research in the lab

The electronic lab notebook eCAT can be configured in many ways.  One of the most common configurations is for the single lab, typically including a lab head, postdocs, students, support staff and possibly  visitors. In this post I’m going to show you a typical model for how to set up eCAT for a lab.  We’ve made a video that covers the same ground, so if you’d rather watch the video, here it is!

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/tutorials/research/research.flv

Lab information basically falls into two categories. First, there is public, i.e., lab-wide, information, such as protocols, supplies, reagants, etc. This can include research data that everyone should have access to. Second, there is information generated by one person and typically thought of as private, or at least only available to others at the discretion of the author. There is a third kind of information, research data related to activities of a group — I’ll consider that later.

Basic eCAT set up

Data in eCAT can be organised to look like this diagram  from Mike Shipston’s lab:

At the top level there are two folders for the two different kinds of information:  Users contains the “private” information, and Lab Resources contains the “public”, i.e., lab-wide, information.

Within the “Users” folder there is a subfolder for each lab member. The lab member can put whatever they want in there, but there will always be a set of folders named for the projects that person is working on, and within those project folders a set of experiment records for each of the experiments that person has done.

Within the “Lab Resources” folder there are subfolders for each of the different types of resource, such as protocols and molecular tools, and within those further subfolders, for examples constructs and oligos in molecular tools.

Sharing

One of the important aspects of this organization of information is the way sharing is set up.

By default, everyone can see inside the Users folder.

Within that folder, the permissions on the individual lab member’s folders are set so that only approved people can see what is in the folder and its children – the individual themselves, and perhaps the lab-head or other supervisor as well. Records below that, such as Projects and Experiments, are set to inherit permissions from their parent records – so they have the same permissions as the individual lab member’s folder.

The Lab Resources folder  does not come preloaded in eCAT and needs to be created. All subfolders of Lab Resources need to be viewable by everyone. Depending on how you want to run the lab, selected people or anyone in the lab will have permission to add records and edit records. For example, permissions on the the Constructs folder can be set so that anyone can add to it or edit records in it, while permission on  the Oligos folder can be set so that only a few users can add to it or edit records contained in it. Again, lower-level records are set to inherit their permissions from their parent record so that they have the same behaviour as is set at the higher level.

Groups

We’ve seen how eCAT can work with individual users. You can  use Groups to make sharing even simpler. For example, you may want to create a group for the members of the lab working on a specific Project.

You might want all the work for that Project to be placed in one folder, with any member of the group able to add records and edit records in that folder. In that case you’d establish a folder Project X in the Projects folder. And for permissions you would create an eCAT group with all the people working on project X in it, and set the Project X folder to give permission to that group to add and edit. An advantage of having the group is that you don’t have to set permissions for each individual.  When someone joins the lab or leaves you can simply  add them to the group or remove them from the group.

Customizing eCAT

So that’s an example of a structure you can use to get your lab working with eCAT. There are also various ways to customize eCAT so that it better fits your work pattern. One simple way to do that is to customize the Favorites menu on the Dashboard page.

The Dashboard lets you quickly see records you have been working on and the Favorites menu lets you filter the Dashboard. So clicking on “My Projects” shows you just the Projects you can see.

You can customize the Favorites menu by clicking on “Customize menus” in your Preferences. You are taken to a page which shows the classes in the system. For example, if you always work with Lab Protocols and want to be able to quickly see them, you can add them to your Favourites menu.  When you return to the Dashboard My Lab Protocols is now visible, and clicking on the My Lab Protocols link shows you just your protocols. This is just one example of how you can customize eCAT by using Preferences!

So that’s a quick overview of organizing lab research information in eCAT. eCAT is incredibly flexible, so an almost infiite variety of  variations are possible.  Why not sign up for a free trial and explore what set ups makes sense for your lab!

The eCAT electronic lab notebook: a time saving technology for labs

Posted by Rory on September 14th, 2010 @ 8:51 pm

Last week eCAT was featured in an article called Time Saving Technology in the Nexxus News Autumn 2010 edition. The other companies featured in the article were:

  1. Actual Analytics, whose technology takes video footage of animals used in scientific research and automatically identifies specific behaviors.  This ensures that data about the animals is captured in an objective fashion, improving the quality of the data on which decisions are made, and significantly reducing the time involved.
  2. Lab901, whose ScreenTape provides a fast solution for automated electrophoresis of DNA, RNA and proteins.

Actual Analytics is about more efficient data capture, and Lab901 is about automated, hence faster, data processing.  The time saving element of each of these solutions is pretty obvious, more or less self evident.  Lab901, for example, says that “On multiple protein and antibody analysis, SDS-PAGE and full analysis can be completed within minutes instead of hours.”  The ROI is readily quantifiable there.  But what about eCAT?  Why did the folks at Nexxus(the Scottish life sciences networking group) decide to include an electronic lab notebook in the company of these two time saving technologies for labs?  I asked Kate Fink, and here’s what she said:

“One of the most consistent things we hear from people and small science businesses is how incredibly busy they are.  Something that saves them time can be a huge benefit . . . so I thought the article could be useful to them . . .  Turns out what tied the [three companies] together to form a cohesive article was their ability to improve efficiency.”

ROI on electronic lab notebooks

It’s a lot harder to quantify the efficiency gains which result when a lab adopts an electronic lab notebook than with the Actual Analytics and Lab901 examples.  Yes, some vendors have done studies concluding that in pharma labs which have adopted an ELN scientists produce and analyze the same amount of data in 80% of the time.   But without being involved in the study it’s hard to know how accurate these conclusions are, and in any event this kind of analysis is not that relevant to PIs in academia, who just don’t think about their labs or their students in these terms.

Decision making in academic labs

So what’s different about academic labs? Here’s a hypothesis:  it has to do with the decision making process.  In pharma labs, although the scientists may be consulted about the possible adoption of an electronic lab notebook, at the end of the day the decision is made by managers and supervisors, not scientists.  Once the decision has been made, training and mentoring will be provided to make the adoption process as painless as possible, but the scientists have no choice but to learn how to use the new system.

In most academic labs, it doesn’t work that way.  Many academic labs are really collections of individual researchers.  In these cases the decision whether or not to adopt an ELN is likely to be truly democratic and collective.  In other cases the PI exercises greater control and there is more of an orientation towards common research.  Even in these cases, however, it’s highly unlikely that the PI will make a unilateral decision about adopting an ELN.  It may be a managed decision, but there will still be strong collective input.

Joshua Shaevitz at Princeton makes the point that “the whole lab has to seriously embrace the new use of technology or the system will fail. Before implementing our wiki system, I setup a mock wiki ELN on my laptop and presented it during lab meeting to show everyone the benefits firsthand. I especially wanted to convince them that the new system would not generate extra work, but would instead make their lives easier.”

Academic labs:  ROI on the process of adoption

This means that for academic labs a key consideration in thinking about ELNs has tobe the the ROI on the process of adoption.  It’s fine to think about the productivity gains — for both individuals and the lab — that will come after the ELN has been adopted.  But these are a pipe dream unless adoption takes place in the first place.  And PIs know that adoption is not going to be easy.  A scientist in a regenerative medicine lab pointed out a typical attitude when he said:

“What amazes me is how little lumpiness there has to be in the use of something for everyone not to want to use it.”

With that attitude to adopting new tools so prevalent in academic labs, PIs know that it will be highly unproductive to attempt to coax, much less coerce, lab members into adopting an electronic lab notebook unless it not only is easy to use but also is easy to learn to use.

Electronic lab notebooks: easier than you think!

Electronic lab notebooks are often perceived to be hard to use, difficult, non-intuitive, and/or things which are only used in commercial settings.  That perception is itself a barrier, but it’s not necessarily a difficult barrier to overcome — with appropriate supporting evidence! — and hence need not be a big drag on the adoption process.  The comment made by Professor Mike Shipston at Edinburgh University (a PI) that

“It was a major surprise; transferring to an electronic lab notebook is actually very easy.”

captures both the typical perception that ELNs are difficult and the reality that adoption of  (in this case) eCAT was very easy.  Andreas Johansson at Lund University (a graduate student), makes the additional point that being easy to get started with eCAT makes it easier to encourage adoption among the lab as a whole:

“The main reason I chose eCAT is because it’s really easy to get started with and use.  If something is hard to get started with and easy to use a lot of people will just have a look at and never get around to starting the first experiment.  eCAT is easy to use; it also means I can ask my colleagues to use it as well.”

Electronic lab notebooks:  a time saving device whose time has come?

I have to say that even I was surprised recently when a new eCAT user, starting from scratch with no prior training or coaching, and completely on his own, created and filled out more than 40 new records, many of which he designed himself, in less than two days, involving only a few hours of work!  When word gets around about experiences like that, perceptions are bound to change, and that means a lower barrier to adoption and a higher ROI on the adoption process.  That’s good news if you’re a PI who is considering adopting a PI for your lab — time saved during the adoption process and time saved once adoption has taken place.

Free electronic lab notebooks: Evernote and eCAT compared

Posted by Rory on September 2nd, 2010 @ 9:19 am

The Personal version of  eCAT is primarily used by postdocs and graduate students who want an electronic lab notebook  tailored to lab work.  In this post I am going to try to unpick the details of what that means — what kinds of things can you do in eCAT that you can’t do in general purpose free ‘ELNs’ (which when you scratch the surface are usually note taking devices of one sort or another)?  As a way of getting at the answers I’ll compare the Personal version of eCAT with the most popular note-taking software, Evernote, which is  used by lots of scientists.

First, some  things the free versions of eCAT and Evernote have in common:

  1. They’re both online and accessible anywhere, anytime.
  2. They’re both used by scientists to record and manage data from their research.
  3. They’re both simple to use.

But here are four things eCAT has that Evernote doesn’t have, and which help make eCAT a great tool for lab scientists:

  1. eCAT “brings structure to your experiments automatically.  Since you are working with project folders you have your own experiments, and you also add protocols, and you add the data and you add whatever electronic stuff you get during the experiments to that folder.  So everything gets sorted by date and time.  It’s much more structure, automatically”.  (Andreas Johansson, Lund University).
  2. eCAT comes preloaded with templates specifically designed for capturing and recording different kinds of scientific research.  There is a generic experiment template, and there is also an  antibody template, a freezer box template, a protocol template, a construct template, etc.
  3. eCAT makes it dead simple to build records of your own design, so you can create structures that allow you to  to effectively capture the kind of research you are doing.
  4. eCAT lets you add files to records.  So for example you can attach a spreadsheet with numerical data relating to an experiment, and confocal images of data which is analyzed in the experiment, to the experiment record.

Those capabilities are pretty useful.  That’s why more and more postdocs and graduate students, like Matt Nicotra at the University of Pittsburgh, are turning to eCAT as an ideal tool for  organizing and managing their experimental data.  Watch Matt talking about how he uses eCAT in this video.

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/user/matt/matt.flv

Making life easy by using groups in the electronic lab notebook eCAT

Posted by Rory on August 26th, 2010 @ 7:00 am

Where to get started when setting up eCAT for your lab?  Probably the first thing you’ll want to do is to create accounts for all the people who will be using eCAT.    That’s simple, and its covered in the User management section of the User Guide.  What next?

All Users group

It’s good practice to set up a group call ‘All Users’ to which all users belong.   Setting up groups is simple, it’s similar to setting up individual users, and its covered in the Group management section of the User Guide.  Why set up a group for all users?  Because it makes your life as administrator so much easier going forward!  Once you’ve got an All Users group, for each new permission you want to set, instead of setting the permissions for that record for each individual user, you simply set the permissions for the All Users group, and all users automatically have those permissions.   Moreover, because permissions in eCAT cascade downward, once you have set permissions for a parent record, those permissions are automatically inherited by all children, and children of children, etc., of that record.  So you only need to set the permissions for a single record and those permissions will hold for all users for that record and all its descendants.  You don’t have to worry about permissions again for that set of records.

Other groups

After you have set up the All Users group, it would be useful to consider how you are planning to use eCAT.  Are there natural subsets of users within the group of people who will be using eCAT?  For example, is there a subgroup in the lab which deals with inventory?  Is there a subgroup which deals with external collaborations?  Are there several subgroups working on different kinds of projects?  Are there two or more labs sharing eCAT?  In these or other similar situations it may make sense to set up one or more groups which  including the people who will be working together on a particular matter or set of matters.  Once you have set up, say, the Inventory group, then you get the same streamlined permissions benefits for the records that Group is working on as were described above with the All Users group.

Flexibility on permissions is always there!

OK, it’s nice that you can deal with permissions in such an efficient way, but what if you want to change things later on or want to do some fine tuning?  No problem, that’s easy too!  Let’s say you’ve set the default permissions for the Inventory group’s records so that everyone in the Inventory group has view and edit permission on the group’s records, and everybody else in the lab has view only permission, because normally you don’t want people who aren’t members of the Inventory group to mess around with records the group creates.  But then the Inventory group sets up a Project that everyone in the lab will be invited to comment on.  To make that possible, all you need to do is to give the All Users group edit permission for that Project.  The All Users group will already have view permission on the Project, by default, and now it will also have edit permission.  Or, perhaps you only want a subset of users to be able to comment on the Project.  In that case you can take an existing group, if there is an appropriate one, or create a new one, and give that group edit permission on the Project.  Then the members of that group, along with the members of the Inventory group, will be able to comment on the Project, and everyone else will only be able to view it.

So groups in eCAT are pretty useful, can save a lot of time, and don’t interfere in the least with eCAT’s flexibility.  In fact they enhance it!

Permissions and sharing in the electronic lab notebook eCAT III: Setting up a project for multiple members of the group

Posted by Rory on August 23rd, 2010 @ 7:00 am

In the previous post and the one before that I covered the basics of the eCAT permissions system and explained how simple permissions work for individual eCAT users.  In this post I’m going to explain how you can set up a Project that multiple members of the lab can work on.  Again we will follow Sarah.  Only this time Sarah is not setting up an experiment  for herself, she is setting up a Project that will be worked on by some and possibly all other members of the lab.

To facilitate this, she sets the scene by not creating a new record directly from the Dashboard.  As we discoverd last time, when she does that the record goes directly into her personal user folder.  Instead she clicks on the Records tab and then on the Projects folder.  Then she clicks Create new, and selects Project.  And this time the project she creates (we’ll call it Group project) appears under the Projects folder.

To set the permissions for Group project, Sarah clicks on Sharing in the menu on the left.  This time she wants to access the full sharing settings, so when the Simple sharing screen appears

Sarah clicks on the ‘here’ link in the text at the top and accesses the full sharing screen for Group project:

This time by default Sarah has a full set of permissions for this record, and no other user — or group of users — has any permissions.  Sarah can then set whatever permissions she wants for each invidividual user.  Perhaps everone in the group will be given view permission, so they can all follow the progress of the project, and active participants will be given edit permission, but only Sarah, as the person managing the project, will have delete and sharing permission.

Since child records inherit the permissions of their parent, all the records that are created in this Project, e.g. experiments, antibodies, protocols, etc., will automatically have the same permissions as the ones Sarah set on the original Group project record.  That keeps things from getting confused.  But if Sarah — and only Sarah because in this case she has only given herself permission to set sharing permission — decides that it’s useful for any particular record that is created under Group Project to have a different set of permissions, then she can reset the permissions for that particular record.

So that’s it!  A quick overview of how to get started creating records in eCAT for your own use and for use by a group, and how to set permissions for those records.

Permissions and sharing in the electronic lab notebook eCAT II: simple permissions for individual eCAT users

Posted by Rory on August 19th, 2010 @ 7:00 am

As noted in the last post, the underlying principle of eCAT’s permissions system is that all records inherit the permissions their parent record has, unless the permissions on the record are reset.  With that in mind, let’s see what happens when a new user creates their first record in eCAT from the eCAT dashboard. You can do that in one of three ways:  by creating a new record, by importing a document, spreadsheet or image, or by creating a record from one of eCAT”s preexisting templates.  In all three cases, the new record will by default be created in your personal ‘user’ folder.  For example, when a new user called Sarah creates her first record, Experiment 1, it is automatically saved in her sarah folder, as shown below.

Like all records, the Experiment 1 record inherits its permissions by default from its parent record, which is the sarah folder. Like all user folders, by default’ sarah’ has all six permissions available in eCAT.  As noted in the previous post, these are:  view, append, edit,  delete, download, and sharing.   So, Experiment 1 has these permissions too, and Sarah can view the Experiment 1 record, edit it, delete it, etc.  Sarah doesn’t need to do anything to make this possible, it just happens automatically in eCAT.

But Sarah has more control that that — she can also change the permissions on Experiment 1 (and of course on other records she creates).  To do that she clicks on ‘sharing’ in the menu at the left of the screen and the following page appears:

By clicking the boxes in Step 1 she can give other eCAT users the ability to view Experiment 1, to edit it, to delete it or to set permissions for it.  And, using Step 2, she can decide which users have these permissions.  Its completely flexible, and well suited to actual lab practices.  For example, Sarah might decide to give view only permission to most members of the lab, and edit permission to another lab member she is working with on Experiment 1 and to the PI, so that the PI can make comments in Experiment 1.  And Sarah has this flexibility for all the records she creates.  If she does nothing they remain private.  But if she wants she can share a record, again in whatever way she wants.

In the next post I’m going to cover sharing and permissions for groups, and give an example of how a lab testing eCAT can set up a Project that multiple members of the lab can work on.

4 ways to get the most out of templates with the electronic lab notebook eCAT

Posted by Rory on July 29th, 2010 @ 7:00 am

Version 3.3 of eCAT, which was released on July 8, comes pre-loaded with more than 20 templates.  Here are four ways to make good use of them:

  1. Get an idea for how other scientists are using eCAT.
  2. Understand the wide range of information that eCAT can help you to manage,  from experimental data to protocols to freezer samples to meeting notes to CHiP extracts to constructs to records about lab personnel and equipment.
  3. Grab a template for your own use; by clicking the “Copy Template” button at the top of the template, you will create an editable copy of the template in your home folder.
  4. Make a blank version of the template; clicking the “Create New” button at the top of the template will create a blank version of the template with the fields not filled in.