Changes to iExperiment an Enterprise Electronic Notebook

The following changes have been made to version 1.1 of iExperiment Enterprise Electronic Notebook (ELN):

• The options for viewing records under the Select tab have been changed. There are now four “List of Records I Can” options: read, edit, delete and download.
  

  Figure 1
  New View Record Options under Select Tab

  Top of Select tab in iExperiment showing the four new “List of Records I Can” options: read, edit, delete and download. The read option has been selected.

• Copy Record, Download Record Archive and Download PDF Archive buttons have been added to the tops of records.
  

  Figure 2
  New Copy Record, Download Record Archive and Download PDF Archive Buttons

  New Copy Record, Download Record Archive and Download PDF Archive buttons at the top of a record in iExperiment.

• Sponsoring Institution options have been added to the experiment properties file. The options are:
  • admin: Where the sponsored institution will be the primary administrator (institution key = 1).
  • author: Where the institution of the author’s active research period will be used.
  • key=: The sponsoring institution key will be identified by its database key; Example key=23

  In this AMI the sponsoring institution option is “admin”.

• Bug Fix: The material Oracle was failing to add materials that lacked a lot or serial number.
• Bug Fix: Sections containing no text, such as a Summary section with only the material produced, were not being displayed from a record archive in a web browser, despite being contained in the record archive.

Evaluating iExperiment an Enterprise Electronic Notebook

It’s easy for you to evaluate iExperiment through Amazon Web Services. A three-part tutorial is available, under the Free Trial tab in the navigation bar above, to guide you through i) the creation of an Amazon Elastic Compute Cloud instance using the iExperiment AMI, ii) configuration of iExperiment, and iii) adding your first researcher.

Browser Compatibility of iExperiment

iExperiment is built on Google Web Toolkit and is not compatible with all browsers. Currently, iExperiment works with Mozilla’s FireFox and Google’s Chrome, but does not work with Microsoft’s Internet Explorer or Apple’s Safari. Both Safari and Internet Explorer suffer from the same two problems:

1. The text editor fails to maintain preexisting text.
2. The file drag-and-drop capability introduces characters into the file names in Safari, and does not work at all in Internet Explorer.

It’s easy for you to evaluate iExperiment through Amazon Web Services. A three-part tutorial is available, under the Free Trial tab in the navigation bar above, to guide you through i) the creation of an Amazon Elastic Compute Cloud instance using the iExperiment AMI, ii) configuration of iExperiment, and iii) adding your first researcher.

Completed PDF Records Implemented in iExperiment

iExperiment is now capable of generating an Adobe PDF document upon the completion of an experiment record. On the first page of the PDF record there is a signature area where both the author of the record and a witness can sign; see figure below. This is suitable for digital signatures, but may not be appropriate if you are still using hand-written signatures. Fortunately, the PDF creation process can be modified to meet these needs.

Figure: Top of a Completed PDF Record

The top of a completed PDF record prepared by iExperiment, Colabrativ’s enterprise electronic notebook. The record has been signed by the author, but has not been witnessed yet.

The creation of the completed record PDF is controlled by an EXtensible Stylesheet Language transformation (XSLT) file that can be modifed to meet the specific needs of the research organization. It is possible to change the XSLT file on the iExperiment server to:

• Add or remove signature lines.
• Change the styling for the record, including the font and font size.
• Add a watermark.
• If the signatures need to be placed on each page, the footer could be changed to contain the signature lines.

Browser Compatibility of iExperiment

iExperiment is built on Google Web Toolkit and is not compatible with all browsers. Currently, iExperiment works with Mozilla’s FireFox and Google’s Chrome, but does not work with Microsoft’s Internet Explorer or Apple’s Safari. Both Safari and Internet Explorer suffer from the same two problems:

1. The text editor fails to maintain preexisting text.
2. The file drag-and-drop capability introduces characters into the file names in Safari, and does not work at all in Internet Explorer.

iExperiment Public Machine Image on the Amazon Management Console

Why We Choose to Use Amazon Web Services

1. Control of Experiment Information: A research organization’s experiment records are the foundation of its intellectual property, and, as such, must be stored in a way that allows the research organization to maintain control over these records. We feel that Software as a Service (SAAS) electronic notebook solutions do not offer the same level of control as having your experimental data on a server you control.
2. Convenience of Cloud Computing: Using an Amazon Machine Image allows us to set up the iExperiment server for you. All you need to do is configure the instance and start the instance’s services. In addition, Amazon’s Elastic Compute Cloud (EC2) is one of the lower cost cloud service providers.
3. Support: Amazon has one of the largest cloud services user communities to draw upon to answer questions that you may have about running your EC2 instance. You can also always contact us at here at colabrativ.com.
4. Server Security: Amazon facilities are Statement on Auditing Standard No. 70 (SAS70) compliant. They completed the Type II audit in 2009, so you know they are doing everything they can to keep your data secure.

Other iExperiment Hosting Options

Amazon Web Services may not be the right solution for you for any number of reasons, including: AWS places the responsibility of the enterprise application setup and maintenance on the client’s administrator; or, you may not be comfortable with the security in a cloud computing environment. If this is the case, you can contact us and we can work with you to install our electronic notebook, iExperiment, either at your facility or at another full-service SAS70-compliant cloud service provider.

In this post and in the following post, I will show you how we setup our enterprise electronic notebook application, iExperiment, on an Amazon EC2 server. This first post covers the launch of the Amazon EC2 server and attachment of Elastic Block Storage volume to the server. The cloud equivalent of purchasing a server and disk, plugging it in, and connecting it to the network. Experienced Amazon EC2 administrators may want to take a quick look at iExperiment Server Requirements and then move on to the second post on the setup and configuring of an EC2 server for iExperiment.

• iExperiment Server Requirements
• Setup of Amazon Web Services EC2 Instance
• Creating and Attaching an Elastic Block Storage Volume (optional)
• Assigning URL of the iExperiment EC2 Server on the DNS Server

In the second post we will go over the setup and configuration of the EC2 server and the installation and setup of iExperiment on it. Topic in the post include:

• Updating the Server
• Installing MySQL
• iExperiment Database Setup
• Mounting Elastic Block Storage Volume (optional)
• SSL Certificate Creation
• Setup Apache & Tomcat
• Adding index.html
• iExperiment Applications Installation

iExperiment Server Requirements

The requirements of our enterprise electronic notebook application, iExperiment, are:

1. Linux hosting web environment: We normally use Apache and Tomcat.
2. MySQL database.
3. Mail server: By default iExperiment uses the iExperiment.net mail server.

In addition to these requirements, we recommend that you have the following before setting up iExperiment.

1. A subdomain name under your domain name for iExperiment, for example iexperiment.example.org.
2. An administrator mail address on your mail server, e.g. admin@example.org.

Setup of Amazon Web Services EC2 Instance

If you are not familiar with Amazon Web Services, we recommend that you read the Amazon Elastic Compute Cloud Getting Started Guide. There you can find instructions on how to sign up for Amazon EC2, which tell you to “Go to http://aws.amazon.com/ec2, click on the Sign Up for Amazon EC2, and follow the on-screen instructions.”

After signing on in the Amazon Management Console, and selecting a region, the following tasks are performed.

1. Select an Amazon Region for the iExperiment Server

   Select a Region from the region pull-down menu at the top of the Navigation panel. We are in Northern California, so we normally select the US West (N. California) region.

2. Create Security Group

   Open the Security Groups panel by clicking on its link under NETWORK & SECURITY in the Navigation panel.

   1. Click on the “Create Security Group” button at the top of the Security Group panel.
      This will bring up the “Create Security Group” popup.
   2. In the “Create Security Group” popup, fill in the following information:
      

      Name:	iExperiment
      Description:	iExperiment open ports: 22 (SSH), 80 and 8080 (HTTP), and 443 and 8443 (HTTPS)
      VPC:	No VPC

      Then click on the “Yes, Create” button.

   3. Click on the iExperiment security group, and click on the “Inbound” tab.
   4. In the “Inbound” tab add the following rules:
      1. From the “Create a new rule” pull-down menu, select “SSH”,
         then click on the “Add Rule” button.
      2. From the “Create a new rule” pull-down menu, select “HTTP”,
         then click on the “Add Rule” button.
      3. From the “Create a new rule” pull-down menu, select “HTTPS”,
         then click on the “Add Rule” button.
      4. From the “Create a new rule” pull-down menu, select “Custom TCP rule”,
         enter the “port range” of 8080,
         then click on the “Add Rule” button.
      5. From the “Create a new rule” pull-down menu, select “Custom TCP rule”,
         enter the “port range” of 8443,
         then click on the “Add Rule” button.
         
         The resulting security table contains the following rules:
         
         
      6. After adding all of the Rules, click on the “Apply Rule Changes” button at the bottom of the Inbound* tab.

    

3. Create Key Pair

   Open the Key Pairs panel by click on its link under NETWORK & SECURITY in the Navigation panel.

   1. Click on the “Create Key Pair” button at the top of the Key Pairs panel.
      This will bring up the “Create Key Pair” popup.
   2. Supply a “Key Pair Name”, then click on the “Create” button.
      Amazon will create the key pair and download the file to you.
      Save the .pem file somewhere accessible to you.

    

4. Launch EC2 Instance

   Open the Instances panel by clicking on its link under INSTANCES in the Navigation panel.

   1. Click on the “Launch Instance” button at the top of the My Instances panel.
      This will bring up the “Request Instances Wizard” popup.
   2. Click the “Select” button to the right of the “Basic 32-bit Amazon Linux AMI 2011.02.1 Beta” under the “Quick Start” tab in the Request Instances Wizard.
   3. Fill in the Instance Details:
      

      Instance Details

      Number of Instances:	1
      Availability Zone:	us-west-1a
      Instance Type:	Small (m1.small, 1.7 GB)

      Then click on the “Continue” button at the bottom of the popup.

   4. We normally change nothing in the “Advanced Instance Options“.
      Click on the “Continue” button at the bottom of the popup.
   5. If you have multiple EC2 instances, you may want to add Tags to the iExperiment instance.
      Click on the “Continue” button at the bottom of the popup.
   6. Choose the “Choose from your existing Key Pairs” option, then select the key pair for iExperiment from a “Your existing Key Pair” pull-down menu.
      Click on the “Continue” button at the bottom of the popup.
   7. Choose the iExperiment security group using the “Choose one or more of your existing Security Groups” option from list of security groups, then
      click on the “Continue” button at the bottom of the popup.
   8. Review the configuration of your EC2 Instance request, then
      click on the “Launch” button at the bottom of the “Request Instances Wizard” popup.
      

   It’s worth noting the id, Availability Zone, and Public DNS of the EC2 instance you created by clicking on the instance in the “My Instances” panel.

5. Create an Elastic IP

   Amazon’s Elastic IP Addresses are static IP addresses that you can associate with an Amazon EC2 server. Open the Addresses panel by clicking on the Elastic IPs link under NETWORK & SECURITY in the Navigation panel.

   1. Click on the “Allocate New Address” button at the top of the “Addresses” panel.
      This will bring up the “Allocate New Address” popup.
      Click on the “Yes, Allocate” button in the popup.
      This will create a new address.
   2. Click on the new Elastic IP address and select Associate Address.
      This will bring up the “Associate Address” popup.
      Select the iExperiment EC2 Instance from the “Instance” pull-down list and
      click on the “Yes, Associate” button in the popup.

   The eleastic IP address will be needed when setting up the Domain Name Server, below, so make a note of it.

Creating and Attaching an Elastic Block Storage Volume (optional)

We highly recommend that you place your experiment records created in iExperiment on an EC2 server in an Elastic Block Storage (EBS) volume. EBS isolates your data from the server failures and its scalable. An existing volume can be copied to a large volume as your iExperiment records increase. From the Amazon Management Console open the EBS Volumes panel by clicking on the Volumes link under ELASTIC BLOCK STORE in the Navigation panel.

1. Click on the “Create Volume” button at the top of the “EBS Volumes” panel.
   This will bring up the “Create Volume” popup.
2. In the “Create Volume” popup enter a volume Size, and Availability Zone.
   The volume Size you choose will primarily depend on the size of the figures and attachment the researchers using iExperiment plan to associate with their experiment records. 10 GiB is a good starting size. The Availability Zone must be the same as the iExperiment instance.
   Click on “Yes, Create” button in the popup.
3. Click on the EBS volume you just created and select “Attach Volume”.
   This will bring up the “Attach Volume” popup with Volume already filled in.
   Select the iExperiment EC2 instance, shown by id, from the Instances pull-down menu.
   Click on the “Yes, Attach” button in the popup to attach the EBS volume to the iExperiment instance.

Assigning URL of the iExperiment EC2 Server on the DNS Server

Here we will use the domain name temp.iExperiment.net, but you will be using a sub-domain of your domain such as iexperiment.example.com. We are using Kattare Internet Services for our DNS server. There we associate the AWS Elastic IP address with both the sub-domain and its secure variant in the iExperiment Zone File:

1. Collaborations with Researchers in Other Organizations

Research is increasingly done on a contract or collaborative basis.  There are even virtual companies that contract out all of their experimentation.  A key feature of our enterprise electronic notebook is iExperiment’s permission management system, which facilitates several ways in which permissions can be set up for collaborations.

• The iExperiment administrator creates a separate institution group for the members of the collaboration in iExperiment’s permission management system. Researchers from the collaborating institution are added to that group. Permissions are set for the collaboration group in such a way that researchers in the group can only view records in that group.  In addition, the administrator can allow researchers and mangers in the sponsoring organization the ability to view the experimental records created during the research.  This allows the team real time access to the progress made by the collaborators on the research.
• The permission management system allows the administrator to assign administrative permissions to a member of a collaborating institution.  This collaborating administrator is only given permission to view records in their organization.  They can add researchers to their organization within iExperiment, thus enabling the necessary personnel to enter experiments.  Again, the collaborator’s researcher will only have access to view records in their organization.  The primary iExperiment administrator can examine who the collaborating administrator has added and what permission they have assigned to various people, including who has been assigned as the project manager.  As described above, the administrator can allow researchers and mangers in sponsoring organizations the ability to view the experimental records created during the research.
• The collaboration enterprise electronic notebook system can be isolated from the internal notebook system, by placing it on a separate server.  Completed records can be easily transferred from the collaboration system to the internal system.

If you are engaged in collaborative research or a virtual company out-sourcing your research, then investing in an enterprise electronic notebook will reduce the time you spend in saving your experimental results, and the experimental information will be more accurate and complete, due to avoidance of a transfer process.

2. Contract Research Organization’s Customer Data

If you are a Contract Research Organization that is interested in helping your customer obtain the greatest value out of the research you provide for them, then you should consider delivering semantic/structure experiment records in addition to human readable research reports.  In iExperiment, the record download method creates a record archive that is a zipped directory containing the XML record and all of the figures and attachments associated with the experiment, i.e. a complete structured documentation of an experiment.  The unzipped record archive can be easily displayed in any web browser using the XSLT transformation supplied in the archive.

The iExperiment administrator in the Contract Research Organization can create a customer group in iExperiment, and add the customer to the group, along with the researchers in their organization performing the research to the group.  The customer access can be restricted to only reading and downloading the completed experimental records or extended to viewing the record in the planning and in-progress states.

Many customers are extremely sensitive to having the research results that the Contract Research Organization is supplying to them mixed with other customer’s information.  This issue can be addressed by setting up a deployment of our enterprise electronic notebook, iExperiment, on a separate server.  A nice customization that can be employed is to use the subdomain of your domain as the URL for this server, e.g. customer_name.CRO_domain.com.

3. Distribution of Sales and Marketing Technical Information

There are a number of situations in which a scientific vendor may want to share technical information with their customers and potential customers, such as:

• Protocols, reagent descriptions and example experiments for kits
• Instrument testing protocols and example results
• Innovative uses of their instrument or kit

For a variety of reasons a scientific vendor may want to control who can view this information.  Our enterprise electronic notebook, iExperiment, allows its administrator to add customers and control the content they can view.  Each test or experiment example can be assigned to one or more categories, and each customer can be granted access to any or all of these categories.

There can be more than one iExperiment administrator.  Sales personnel could be set up as secondary administrators, thereby allowing them to quickly add a potential customer to iExperiment, and send an email containing links to tests or example experiments that the potential customer would be interested in.  In addition, an automated procedure could be created that allows a potential customer to gain access to particular tests or example experiments by signing up on the scientific vendor’s web site.

iExperiment has several functionalities that would be useful to a customer.  First, they can create a new experiment record based on an existing record using the “Copy Record” method.  The “Copy Record” method does not copy the record’s results, summary or conclusion sections.  Second, they can download the complete experiment record including all of its figures and attachments.  This allows the customer to perform additional analysis on the data in the experiment record.  The iExperiment administrator controls the ability to download a complete experiment record, so it can be turned off completely or only granted under certain circumstances.

If the scientific vendor’s development lab is also using our enterprise electronic notebook, iExperiment, then their experiment records can easily be made available to the customers.  This can be done within a single deployment of iExperiment, through the use of an additional experiment state “release to customers” that could require sign-off by someone other than the researcher that worked on the experiment.  This could also be implemented using a transfer protocol between the development lab’s iExperiment deployment and a second iExperiment deployment that the customers have access to.

Finally, a customer community could be set up using iExperiment.  Customers could post and share the details of innovative new uses of the vendor’s equipment or kits.

When a file is dropped on an iExperiment record, the application examines both the file type and dropped file location on the experiment record to determine how to handle the dropped file. Generally, the contents of a dropped file are added below the section it was dropped on. If iExperiment cannot determine where to place the information, a popup message informs the user of this issue, and the dropped file is not included in the record. A number of file types can be processed by iExperiment including:

	Image Files: When an image file is dropped on to an experiment record, the file is placed in a figure box. iExperiment will give a default title above the image and a default caption below the image. Both the title and the caption can be edited. Most image file extensions are recognized and placed in figures, except for TIFF files due to the lack of support in web browsers for this file type.
	Image Files: Text Files: When a simple .TXT text file is dropped on to an experiment record, three options are offered:  The file can be stored as an attachment and displayed in an attachment box with a title to the right of the file icon and a caption below the icon and title. Like figures, both the title and the caption can be edited. The file can be saved as an attachment and the contents added as the attachment caption. The file can be placed in a text section. In this case, the file will not be saved as an attachment but added as part of the text.
	XML Files using iExperiment’s Schema: Full records, parts and materials can be added using iExperiment’s XML schema, which can be found at www.iExperiment.net/XML.
	iExperiment CSV Files: Lists and tables are added to experiment records using a comma-separated values (CSV) format.  The CSV file can be dragged and dropped on to a section in a record, or added using a menu.  A tutorial on the creation of CSV files for iExperiment can be found at www.colabrativ.com/csv-table-creation/.
	Other Files: All other files that are dropped on to an experiment record are stored as attachments. Attachments have a title and a caption, both of which can be edited. iExperiment recognizes and displays the appropriate icon for a number of file extensions, including Microsoft Office, Adobe’s PDF, VectorNTI and Protein Data Bank files.