FAQ - Frequently Asked Questions¶
Collections¶
What is a sample in LabID?
In LabID, samples represent various materials like cells, stools, or parts of organisms. These samples can be linked to a single parent specimen or to multiple parent samples. When a sample is linked to one or more parent samples, we refer to it as a "sample" or "derived sample". LabID allows flexibility by not requiring samples to be linked to a specimen, which is helpful when the specimen is obtained from an external source. The path from a sample back to its original specimen or sample(s) is known as the "Sample Lineage".
Samples in LabID are categorized by their types, known as "Sample Type". By default, samples are categorized as "Sample", but they can also be classified e.g. as "sequencing library". LabID administrators can customize the list of available sample types to better suit the needs of their research.
Find more information at Getting Started > Collections > Samples
What are the differences between Experiments, Protocols and Assays in LabID?
In LabID, an "Experiment" is like a journal entry for your lab work. It records applying a "Protocol" to a set of samples. Think of a Protocol as a recipe for a specific experiment—it gives you a general idea of what to do. An Experiment builds on this by adding details on how the recipe was followed and documents the results, quality control measures, conclusions, and any new hypotheses derived from the experiment. An Experiment can also produce samples, datasets, or nothing at all—it's pretty flexible and can cover any experimental procedure.
On the other hand, an "Assay" represents a specific, well-defined type of experiment, like "Illumina Sequencing". For an Assay, you need to provide inputs, outputs, and specific details. Each Assay has a type, such as "Illumina Sequencing". It also requires a Protocol of a matching type, directly linked to the Assay type. This might seem a bit redundant, but it's useful because it allows LabID to store Assays and their results, even if there wasn't a journal entry for them. This is handy for managing raw data, like NGS data, even if you're not using LabID's Electronic Laboratory Notebook (ELN) functionality.
The "Protocol Type" (like extraction, growth, or library preparation) is somewhat connected to the Assay type. However, Experiments don't have a specific "experiment type" because they're more loosely defined. The Protocol type is more for organizing your lab's procedures, while the Assay type explicitly states what kinds of samples it accepts and what type of dataset it produces, among other details.
What are Protocols and Protocol Lists in LabID?
In LabID, a "Protocol" is a set of instructions detailing how to perform a specific task in the laboratory. A "Protocol List" is a structured sequence of these Protocols, arranged in a specific order. Each sample in LabID is associated with its own Protocol List, known as the "Experimental Procedure", which outlines the steps involved in producing the sample from its immediate parent, whether it's a Specimen or another Sample. If no parent is specified, the procedure encompasses all steps from the unspecified specimen.
Notably, a Protocol List links directly to Protocols rather than possessing its own copy. Therefore, any modifications made to a Protocol impact all samples referring to it through their Protocol List, ensuring consistency across experiments. Additionally, LabID offers "Protocol List Templates", predefined collections of ordered Protocols that can be reused. These templates streamline the process of setting up Protocol Lists, especially when configuring multiple samples simultaneously. However, alterations made to a Protocol List Template do not retroactively affect samples already utilizing that template. Each sample's Protocol List is a distinct copy of the original template, maintaining independence from subsequent template modifications.
What are studies in LabID?
A study is an assay collection as defined by the ISA specifications.
What are Projects LabID?
A project is more broadly defined than a study. It contains links to many studies and potentially other information (members, templates, etc.).
How can I add a new protocol type?
LabID can be customized to add for example, new stock or protocol types. These will have to be added by your admin. See the admin doc.
Permissions¶
Someone shared a link with me, but access is denied. Why?
Every object has its own permissions set, which can be seen at the bottom of the item detail page. Typically the owner of the object has to grant others access to the item. If you are in the same group, then generally you will be able to see each others items.
I'm looking for chemical X, but I can't find it in LabID, how come?
By default, all items are only visible to members of the same group. Only (publicly) shared items can be seen by others.
Search¶
I know item X exists in LabID and is shared with me, but I don't see it. How can I find it ?
Make sure that on the list page you toggle All items, alternatively use the global name search.
Miscellaneous¶
I'm receiving a lot of ⚠️ LabID: Overdue experiments emails, can this stop?
To stop receiving these emails set the correct estimated completion date (link to experiment life cycle). It is important
to properly flag your experiments as completed or failed so they get automatically frozen and signed (for IP purpose).
Availability¶
Can a group leader leaving EMBL get a special license to continue using LabID?
No special license is required, LabID is now open source. But they will have to host their own LabID instance, which will only contain data they are allowed to take with them.
Is LabID available outside EMBL?
- Our EMBL installation is currently under VPN for security reasons. So it is currently not available to the outside.
- LabID is free and open source so people are able to deploy LabID installation at their own sites.
Is LabID open-source?
Yes, the different projects are visible on Gitlab, Lab Integrated Data Project
How do I validate a timestamp?
Every attachment and autogenerated PDFs gets Time Stamped. Once an Experiment is frozen, a ZIP is generated and this ZIP will contain among the relevant HTML and PDF files, all timestamp information.
- To see information about a timestamp:
- To validate that the document is identical to the one that was timestamped:
# first download the DFN specific verifier (see also https://blog.pki.dfn.de/2016/04/zeitstempeldienst-der-dfn-pki-jetzt-mit-sha-2-signaturen/)
wget https://info.pca.dfn.de/doc/timestampverifier-latest.tar.gz
tar -xzvf https://info.pca.dfn.de/doc/timestampverifier-latest.tar.gz
cd timestampverifier-1.1
# create a request for the file you want to validate
openssl ts -query -data ../MyExperiment.pdf -no_nonce -sha256 -cert -out request.tsq
# now validate against the timestamp response that was included in the ZIP
java -cp libs/bcpkix-jdk15on-152.jar:libs/bcprov-jdk15on-152.jar:. de.dfncert.timestampverifier.TimeStampVerifier request.tsq ../MyExperiment.pdf.tsr chain.txt rootcert.crt crl.txt