Labii electronic lab notebook (ELN) and laboratory information management system (LIMS)

Sunday, March 10, 2019

Labii ELN &LIMS Introduces New Reference Management Function

Reference management software help authors and other scholars to record and make use of bibliographic citations. They also help in the management of project references either as a company or an individual.

Proper referencing is super important in research and the pharmaceutical industry, in particular, to facilitate fact verification and enhance the concreteness of procedures as well as findings in the laboratory.

Labii's unwavering mission to simplify the activities of scientists and promote transparency in scientific research with ELN and LIMS keeps making ground-breaking progress. The most recent development is in the domain of reference management functionalities.

To make referencing possible, Labii has introduced new widgets: PMID, PubMed Abstract, and PubMed Citation.

What is PubMed?


PubMed is a free search engine which provides primary access to the MEDLINE database of references and abstracts on life sciences and biomedical topics. The database is maintained by the United States National Library of Medicine at the National Institutes of Health as part of the Entrez system of information retrieval.

In addition to being used to document new scientific data, Labii ELN & LIMS can now help you managed the published papers from PubMed. 

New Reference Management Features of Labii ELN & LIMS


PMID is a Column type widget which stores PubMed ids and synchronizes other fields with PubMed. The Table below shows various fields that can be added


Column
Widget
Description
PMID
PMID
PubMed id
journal
Text
Journal title
volume
Number
Journal volume
issue
Number
Journal issue
pages
Text
Journal pages
authors
Text
The authors
pubdate
Text
Published date
pmc
Text
PMC id
doi
Text
DOI
full_text_link
Text
Link of full text


PubMed Abstract and PubMed Citation are section widgets. The former displays the abstract of a paper after checking to ensure it has been downloaded. It will automatically download and save the abstract in the database if it has not been downloaded. The PubMed Abstract widget replies on the PMID widget to query the abstract and provides an error message if the field is missing.

The latter displays the summary for multiple PMID’s and can be inserted into multiple experiments or protocols. It doesn’t reply on PMID widgets.

You can add a list of PMIDs by clicking on the edit icon and then pasting a list of PMIDs separated by “,” or on PMID per line.

How to Create Your Own Reference Manager in Labii


Labii’s new function to manage references is easy to use as your own reference manager, once you get familiar with the configuration and use.

Configuration


  1. Start by creating a table; papers
  2. Add PMID columns and all other related columns as described above. 
  3. Labii ELN &LIMS Introduces New Reference Management Function
    Labii Column Configuration for Reference Manager
  4. Add Abstract section to default section with widget PubMed Abstract.
    Labii ELN &LIMS Introduces New Reference Management Function
    Labii Section Configuration for References Manager
    1. Add Full Text section to default section with widget Files (No Preview).

    How to use


    1. After adding a new paper, type any string to the title. 
    2. Provide correct PMID
    3. Click the Submit button to submit. 
    4. The page will redirect to the detailed view of the paper, and the abstract will be updated automatically. 
    5. Click the “sync” next to the PMID to download the paper title, journal, authors, etc. from PubMed. 
    6. Upload full text to Full Text section. 

    You can go on to add other fields to enhance reference management. For instance:

    • is_read – can be added to check whether a paper has been read. 
    • category – to track the category of the paper etc.


    Also, the import function can be used to batch import all PMID.

    Benefits of Using Labii’s Reference Management Software


    • All data is stored in one repository. 
    • Citations can be inserted to the protocols/experiments in Labii ELN & LIMS 
    • Additional notes can be inserted for each paper.


    Labii ELN & LIMS is different from other reference managers. Although it now provides reference management functions as an additional utility, it wasn’t designed to replace any of the reference managers in the market as it doesn’t allow the insertion of citations when writing an article.

    Monday, January 14, 2019

    Sample Consumption Tracking Functionality in Labii ELN & LIMS

    Sample Tracking


    Scientists need all the help they can get and Labii’s dedication to this course continues to result in huge strides towards making biotech research much easier, transparent, and reliable. Another new function is here and users of the unique data management software should be excited because it’s only getting better.

    The most recent advancement of the already practical ELN & LIMS concerns sample consumption which is the record of sample or reagent usage in a biotech laboratory.

    According to GLP (Good Laboratory Practice) and FDA 21 FR Part 11 requirements, sample consumption must always be captured and recorded during scientific experiments. These records are potential guides to other scientists trying to follow and reproduce the results. They are also critical to identifying problems in case something goes wrong.

    Tracking sample consumption is a generally challenging process especially in ELN (Electronic Lab Notebook) and LIMS (Laboratory Information Management System). However, Labii has succeeded to make it very simplified and easy for researchers. It makes use of both ELN and LIMS functionalities. This complex requirement is responsible for a majority of ELN or LIMS products in the market lacking sample consumption capabilities. All samples and reagents are stored in the LIMS, whereas, consumption occurs during the experimentation process. 

    With eyes on this challenge for scientists, Labii ELN & LIMS has come up with an amazing solution which combines data management for both ELN and LIMS in one easy to use online repository.

    Labii’s flexibility of data storage and the capacity to incorporate new functionalities has permitted the cutting-edge introduction of this new feature. Now, tracking sample consumption has become possible and easy to document.

    Below is a breakdown on how to configure your Labii ELN & LIMS account to store the sample consumption details. You can find the full details at Labii Documentation.

    Before you can start making use of Labii’s sample consumption tracking functionality, your administrators are required to make certain configurations. 

    First, you must create three tables namely; 
    1. Experiments – table to contain a list of experiment notes
    2. Samples – table to contain a list of samples
    3. Consumptions – table to contain tracked values of consumption details 
    After creating the three tables above, additional tables can be created. For instance, a Reagents table can be created to track the consumption of the reagents. 

    3 Tables for consumption tracking
    3 Tables for consumption tracking
    The Experiment and Samples tables don’t require any specific fields. Meanwhile, you will need to create the following fields for the Consumption table:
    • experiment, the experiment id
    • sample, the sample id
    • amount, how much is used
    • unit, the unit of consumption

    The picture below shows how you should choose the widget and default value. 

    Columns for the Consumption Table
    Columns for the Consumption Table
    You don’t have to set the default value for the sample column if you want to track consumption for other tables as well. 

    Separate the Unique Code with "," for the default value if you want to track the consumption for multiple tables. For example, use "SP,RG" to tracking both samples and reagents.

    Now, the columns in the Consumption table creates all necessary links between experiments and samples. The details of consumption can be displayed in an experiment or a sample with the help of Backlink widget. 

    Tracking Consumption

    After completing your configuration as outlined above, you can view the consumption at two different levels:

    • The experiment level to see how much samples are being used in a particular experiment
    • The sample level to track how many experiments are using this sample. 

    CLICK HERE for more details on how to track consumption at both the experiment level and sample level.

    The process is so easy to master and it presents an amazing utility tool to all biotech research laboratories. 

    Shirley Scott


    Monday, January 7, 2019

    Announcing the Historic Partnership between Labii and Hanhai Biolabs

    It’s no longer alien that the future of effective data management in the pharmaceutical industry and research lies in technological innovation with Electronic Laboratory Notebooks (ELN) and Laboratory Information Management Systems (LIMS).

    The 19th of November, 2018 saw two relentless advocates of simplifying the work of scientists and researchers across the globe partner with each other i.e. Hanhai Biolabs and Labii. The partnership aims at bringing ELN & LIMS to the doorstep of startups in Hanhai Biolabs.

    Announcing the Historic Partnership between Labii and Hanhai Biolabs


    This partnership move is a step in the right direction, in line with Hanhai BioLabs’ commitment to their mission of promoting interaction among global innovation resources. It also makes the case for their dedication towards becoming a respected, world-class life science accelerator.

    Hanhai BioLabs Accelerator provides life science startups with seed funding, mentoring services, office spaces and other resources required to establish with continuous positive impact into the industry. After 6-months of acceleration, what they do is graduate and build possible alliances with other industry partners for sustainability and further fundraising with VC partners.

    With resources grouped into three main categories namely; Services, Mentorship, and Capital, Hanhai BioLabs offers startups with direct access to a life science-related network of leading research institutions, industries, investors and product channels. This is in addition to the technical support on offer from experienced mentors and free office spaces for up to 6 months.

    Striving to be a leader in life sciences, the state-of-the-art startup ecosystem they have succeeded to setup continues to empower innovators across the globe from their San Francisco, Bay Area location. With this, they get the support needed to build sustainable businesses to solve the most challenging problems in life sciences.

    Also located in the San Francisco Bay Area, Labii is a startup helping scientists from biotech and the pharmaceutical industry with a ground-breaking ELN software to document, manage, and interpret research data. Labii’s aim is to accelerate scientific discovery by eliminating the bottlenecks in the generation of data, documenting and processing.

    Affordability is a huge problem for most other ELN & LIMS software especially for startups, and with the potential of making things super easy and transparent at a much cheaper rate, Labii’s ELN is unique.

    The announced partnership between Labii and Hanhai BioLabs will be very beneficial to biotech startups. Aligning their missions and efforts looks set to ELN & LIMS which are usually too expensive for startups much more affordable. Hanhai BioLabs startups will have the luxury of documenting and organizing their research data from day 1 with Labii ELN & LIMS. The startups who prove to have valuable data will be more likely to be successful and get funded.
    The amazing utility of Labii’s software and continuous flexibility to update is a gem of an attribute, especially in today's fast-changing technological world.

    Shirley Scott