Morgan Taschuk reviewed the original version of this manuscript published, which was submitted under a different title "NanoLIMS, A Simple Open-Source Laboratory Information Management System (LIMS) for Small Sequencing Labs". This version was rejected, revised and re-submitted. 

Review is as follows:

NanoLIMS is an open-source laboratory information management system for small sequencing labs. Its claims include: it is free; easy to set up, customize and maintain for users who are not heavily technical; and allows flexibility in the fields that are recorded. Some basic reporting is built in. It is written in PHP and uses a MySQL database, is intended to be deployed on a private network.

Small labs on the cutting edge of research require flexibility for recording sample information and have specific and unique data collection requirements. NanoLIMS claims to be a flexible and general purpose LIMS, but this is not evident in the figures or the NanoLIMS interface. NanoLIMS is set up with default sample fields, transitions and naming schemes. Its conceptual model for how samples are recorded is shown in Figure 3, supplementary figures 2, and 3, but these figures have no text description to accompany them. Some of the terminology is unfamiliar, and so must be explained either in the text or the documentation. The current LIMS is clearly intended for environmental metagenomics, but this information is never shared in the text.

For example, the default fields when adding a sample include "location", "relative location", "collector name", and "samplers". I MUST enter these values in order to proceed. In addition, there are fields for "flow rate" and "height above floor". The "Daily Data" is for measuring the output from a number of sensors at a particular location, which is not something required for an NGS LIMS. The concept of "sampling" seems very tied to sampling from water or air: the "add sampler" page even has a tooltip that says "What is an Air Sampler Identifier?".

In order to validate the claims of the software itself, I installed and tested NanoLIMS on my own computer.

Free: The code is freely available on Github, and also able to be downloaded as a ZIP if a user cannot use git for whatever reason. The GPL3 license is clear and available in the repository.

Easy to set up, customize, and maintain: The authors claim that it works on Chrome and Firefox, but do not mention Internet Explorer. IE is the preferred browser for many researchers and so NanoLIMS should be tested in the most recent IE version. I had considerable difficulty setting up NanoLIMS on my own computer. I sent the authors a request for assistance via a bug report, and our interactions are in Issue #1 on the Github tracker: The corresponding author has been very responsive, but it took six interchanges to be able to log in to the system. There were several errors in the documentation and at least one SQL error that I found. I would not have been able to debug the application without prior knowledge of debugging MySQL and Apache. As for it being easy to customize, the fields that the admin user can edit are called one thing in the "Update Dropdown" screen and another in the forms, e.g. "Quant Instruments" versus "Instrument/Kit Used to Measure DNA Concentration:". This is not terrible as long as the documentation clearly shows the mapping, but it does not.

Flexible: "Admin users are able to add up to 10 custom entries" (line 185). Why limit the number? If for cosmetic reasons, consider fixing the interface rather than requiring users to modify their entry to fit the arbitrary limit. I was able to add and edit entries into the LIMS without any problems. The one concern that I have about flexibility is that the possible fields are fairly rigorously defined by database tables, and are perhaps specific to the authors' lab or institution. There is a table called "Relt location", for example. There is no documentation as to what these tables mean. They can be hidden using the admin menu if not required.

Overall: Setting up NanoLIMS was difficult and required contacting the authors. The lack of documentation makes customization difficult. Although there are manuals describing how to work with the LIMS, there is no overall explanation of the concepts that underlie NanoLIMS. This information is essential for the small lab starting with a LIMS for the first time. The LIMS is designed for metagenomics sequencing and many screens, fields and default values are specifically for that purpose, but it is never stated in the text. A lab that sequences solid tissue, biobanked samples or blood would need to customize most of the interface, and the documentation is not complete enough easily do so.

NanoLIMS should either become more a more generic LIMS or declare itself as a metagenomic LIMS. Regardless, it requires better documentation to support its claims of flexibility.

Level of interest
Please indicate how interesting you found the manuscript:
An article whose findings are important to those with closely related research interests.

Quality of written English
Please indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?
Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?
Do you hold or are you currently applying for any patents relating to the content of the manuscript?
Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript?
Do you have any other financial competing interests?
Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I work on MISO LIMS, another open source laboratory information management system.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published.
I agree to the open peer review policy of the journal.

Authors' response to reviews:

Reviewer #1: The authors present NanoLIMS, a free and open source LIMS. The authors correctly identify the lack of
a low-cost LIMS system as an important limitation for many small labs. I have one serious concern about this particular
system however, and that is the installation process. The authors advertise in their abstract that this system is intended
for labs that may not have dedicated IT personnel. This means that the system must be easy to set up for biologists who
likely have no command line experience. The online install instructions then begin by pointing the user to googling LAMP
setup (which inevitably, I think, will be a command line driven process) and then a series of command line sets for setup.
I think the authors need to make this system available as a binary for ease of installation (e.g., Anaconda is becoming
very popular for binary distribution, and should work for this) or revise their claims about the system to indicate that it
will require a system administrator to setup and maintain (e.g., install updates to NanoLIMS or the underlying LAMP
stack).
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Author response:
To address the difficulty in deploying MetaLIMS (formerly NanoLIMS), the authors have created a second type of
deployment and improved documentation to remove some of the complications associated with webdeployment.
Suggestion by authors for the use of web hosted systems removes difficulty for users managing
and securing their own web server as well as the task of backing up data. Inclusion of bash scripts to install
required prerequisites and MetaLIMS make deployment using this method a 2-3 step process, therefore
significantly reducing the aforementioned deployment complexity.

I have several other smaller comments.
First, I recommend a more permissive license than GPL, which prevents integration with other non-GPL licensed
software. LGPL and BSD are more permissive choices. A good discussion of this can be found here:
/>-------------------------------------------------------------------------------------------------------------------
Author response:
GPL license not changed - Decision by authors not to change the GPL License with MetaLIMS (formerly
NanoLIMS). Current understanding of GPL software license includes that if you use GPL software, your project
must also be released under the same license
(). Due to the inclusion of PhpExcel with is
under the GPL license, MetaLIMS is also being released under the GPL license.
-------------------------------------------------------------------------------------------------------------------
Next, I recommend that the authors make a demo video that can be included as a supplementary file. This will be useful
for demonstrating what the system can do.

-------------------------------------------------------------------------------------------------------------------
Author response:
Improved documentation without video - There was a split between authors and colleagues on whether to
include a demo video. Many felt that they personally did not in general benefit from watching demo videos.
Decision was to forgo creation of demo video in lieu of improved documentation on GitHub.
-------------------------------------------------------------------------------------------------------------------
There are currently no releases available on GitHub. The authors should produce official releases on GitHub to support
reproducibility.
-------------------------------------------------------------------------------------------------------------------
Author response:
Release of MetaLIMS (formerly NanoLIMS) at GitHub has been created.
-------------------------------------------------------------------------------------------------------------------
Finally, the figures are very blurry, for example Figure 2 is illegible.
-------------------------------------------------------------------------------------------------------------------
Author response:
Figures have been changed. Original Figure 2 no longer exists. Image size and dpi for all images have been set to
the formatting standard as outlined in the GigaScience submission guidelines.
-------------------------------------------------------------------------------------------------------------------
Reviewer #2: I, Robert Davey, promise:
- to not hide behind a screen of anonymity
- to be open and honest with you (the authors) at all times
- to be constructive in my criticism
- within the rules given to me by the journal, to assist you in every way I ethically can to get your manuscript published,
by providing criticism and praise that is valid and relevant
The technical note outlines "NanoLIMS, A Simple Open-Source Laboratory Information Management System (LIMS) for
Small Sequencing Labs", a web-based software tool to aid sequencing labs in sample tracking through lab processes.
The paper is generally clear with no major issues in terms of structure, content, or conventions regarding code
availability. The code is freely available on GitHub under the GPLv3, and there are adequate user and developer
documentation pages to assist. The GitHub repository has a license.md and README.md.
However, I do have some minor comments:
- There are a much larger number of available LIMS, some very much overlapping with the author's list of NanoLIMS's
features. A comprehensive list is here: . Whilst I wouldn't expect a complete review
of all existing LIMS to be necessary, I would at least expect the recently updated open-source versions be compared to
NanoLIMS. For example, sierra LIMS, MISO (I will note that I am the original developer of MISO), Bika, and MendeLIMS
are all open source and are available as sample tracking LIMS from the outset. It would be helpful to understand how
the feature set of NanoLIMS compares to those of these tools to enable potential users to understand the benefits of
NanoLIMS in their labs.
-------------------------------------------------------------------------------------------------------------------
Author response:
Added comparison of MetaLIMS (formerly NanoLIMS) to recommended open-source LIMS to help define the
differences between current LIMS and MetaLIMS (see Table 1).
-------------------------------------------------------------------------------------------------------------------
- NanoLIMS is promoted as a simple and low-maintenance LIMS that is suitable for labs with little or no IT provisioning.
Upon reading the developer documentation, it becomes clear that NanoLIMS has no delete functionality available to
users within the web interface (e.g. />Instead, a DB admin has to manually delete rows from relevant tables to remove
samples/pools/etc. This isn't user friendly, is prone to error, and these limitations should be explcitly mentioned in the
manuscript to better inform users of current functionality and proposed future improvements.
-------------------------------------------------------------------------------------------------------------------
Author response:
The decision to not include a delete function was made in order to prevent accidental deletion of samples and to
ensure posterity of sample collection. While no delete function currently exists, the users are able to easily edit
samples to make corrections in date, project name, and sample number. This limitation is now explicitly stated
in user documentation for both users and admins.
-------------------------------------------------------------------------------------------------------------------
- The database schema supplied with the software uses latin1 encoding, rather than UTF-8. Many international
characters will be unsupported using this encoding. The authors should strongly consider updating their code and
schemas accordingly to allow a broader international user community to use their software fully.
-------------------------------------------------------------------------------------------------------------------
Author response:
Updated tables to charset utf8 and collation type utf8_unicode_ci
-------------------------------------------------------------------------------------------------------------------
- It is unclear from the manuscript if NanoLIMS supports the actual submission of read data to public repositories, or
simply that users are able to retrospectively add an INSDC accession after submitting the reads manually via a
SRA/ENA/DDBJ service. This should be clarified.
-------------------------------------------------------------------------------------------------------------------
Author response:
Clarified in documentation and manuscript that read data submission is only for recording and not for actual
submission.
-------------------------------------------------------------------------------------------------------------------
- I am unclear as to why the authors have chosen a 20-field limit (10 text, 10 numeric) for user created information.
From the supplied database schema, it seems that this is due to 20 specific rows in a specific table. This could easily be
refactored to allow any number of user-created fields of any type (alphanumeric). Is there a reason the authors chose to
limit the user fields to this arbitrary amount?
-------------------------------------------------------------------------------------------------------------------
Author response:
Restriction to 20 custom fields removed. MYSQL tables re-designed to store unlimited number of fields.
-------------------------------------------------------------------------------------------------------------------
- Whilst the manuscript does state that NanoLIMS has been used in a local installation and hasn't been tested in a live
internet environment, the authors are using dangerously insecure code to generate password reset keys, i.e. rand().
Specific libraries exist to generate keys based on more secure PRNG code, e.g. openssl_random_pseudo_bytes(). This
code should be updated.
-------------------------------------------------------------------------------------------------------------------
Author response:
Key generation for reset password token is changed and now uses more secure random_bytes() function
() in lieu of the suggested openssl_random_pseudo_bytes()
-------------------------------------------------------------------------------------------------------------------
- NanoLIMS makes heavy use of XLS templates. To enable wider use, the authors should consider the use of CSV to avoid
Excel versioning issues and non Excel users. However, this is not a point that affects my recommendations for
acceptance of this manuscript as I realise the relative ubiquity of Excel.
-------------------------------------------------------------------------------------------------------------------
Author response:
File format for downloaded files has been changed to tab-delimited files (.txt) to remove problems with excel
versioning and those without access to Excel. Tab delimited files can still be opened and manipulated in Excel as
needed by users.
-------------------------------------------------------------------------------------------------------------------
Reviewer #3: NanoLIMS is an open-source laboratory information management system for small sequencing labs. Its
claims include: it is free; easy to set up, customize and maintain for users who are not heavily technical; and allows
flexibility in the fields that are recorded. Some basic reporting is built in. It is written in PHP and uses a MySQL database,
is intended to be deployed on a private network.
Small labs on the cutting edge of research require flexibility for recording sample information and have specific and
unique data collection requirements. NanoLIMS claims to be a flexible and general purpose LIMS, but this is not evident
in the figures or the NanoLIMS interface. NanoLIMS is set up with default sample fields, transitions and naming schemes.
Its conceptual model for how samples are recorded is shown in Figure 3, supplementary figures 2, and 3, but these
figures have no text description to accompany them. Some of the terminology is unfamiliar, and so must be explained
either in the text or the documentation. The current LIMS is clearly intended for environmental metagenomics, but this
information is never shared in the text.
For example, the default fields when adding a sample include "location", "relative location", "collector name", and
"samplers". I MUST enter these values in order to proceed. In addition, there are fields for "flow rate" and "height above
floor". The "Daily Data" is for measuring the output from a number of sensors at a particular location, which is not
something required for an NGS LIMS. The concept of "sampling" seems very tied to sampling from water or air: the "add
sampler" page even has a tooltip that says "What is an Air Sampler Identifier?".
-------------------------------------------------------------------------------------------------------------------
Author response:
Scope of MetaLIMS (formerly NanoLIMS) redefined to be specifically for small metagenomics labs prior to input
into NGS sequencing pipelines and is now defined as such in the manuscript and in the GitHub wiki.
Fields specific to authors lab, "flow rate" and "height above floor", are removed. "Air Sampler Identifier” is
corrected to "Sampler Identifier".
-------------------------------------------------------------------------------------------------------------------
In order to validate the claims of the software itself, I installed and tested NanoLIMS on my own computer.
Free: The code is freely available on Github, and also able to be downloaded as a ZIP if a user cannot use git for
whatever reason. The GPL3 license is clear and available in the repository.
Easy to set up, customize, and maintain: The authors claim that it works on Chrome and Firefox, but do not mention
Internet Explorer. IE is the preferred browser for many researchers and so NanoLIMS should be tested in the most
recent IE version. I had considerable difficulty setting up NanoLIMS on my own computer. I sent the authors a request
for assistance via a bug report, and our interactions are in Issue #1 on the Github tracker:
The corresponding author has been very responsive, but it took six
interchanges to be able to log in to the system. There were several errors in the documentation and at least one SQL
error that I found. I would not have been able to debug the application without prior knowledge of debugging MySQL
and Apache. As for it being easy to customize, the fields that the admin user can edit are called one thing in the "Update
Dropdown" screen and another in the forms, e.g. "Quant Instruments" versus "Instrument/Kit Used to Measure DNA
Concentration:". This is not terrible as long as the documentation clearly shows the mapping, but it does not.
-------------------------------------------------------------------------------------------------------------------
Author response:
Not extensively developed on IE - Due to many versions of IE and larger differences in old IE with current
browser standards, MetaLIMS (formerly NanoLIMS) has not been extensively developed for use with IE.
However, on cursory tests, MetaLIMS works correctly with the new Microsoft Edge .
Secondary installation documentation suggesting use of web-hosting and author created bash scripts, removes
many of the troubles encountered by reviewer3 in GitHub issue #1 by setting the correct environment variables
and prerequisites needed for correct deployment with minimal need for user input. Additionally, full manual
installation documentation used by reviewer3 was updated to call out these needed prerequisites. Specific
errors called out by reviewer3 in issue#1 regarding the documentation were corrected.
Field names updated to match naming convention in "Update Drop Down" screen.
-------------------------------------------------------------------------------------------------------------------
Flexible: "Admin users are able to add up to 10 custom entries" (line 185). Why limit the number? If for cosmetic
reasons, consider fixing the interface rather than requiring users to modify their entry to fit the arbitrary limit. I was able
to add and edit entries into the LIMS without any problems. The one concern that I have about flexibility is that the
possible fields are fairly rigorously defined by database tables, and are perhaps specific to the authors' lab or institution.
There is a table called "Relt location", for example. There is no documentation as to what these tables mean. They can
be hidden using the admin menu if not required.
-------------------------------------------------------------------------------------------------------------------
Author response:
Limitation of number of custom entries is removed. Table names renamed to give clearer meaning to what they
are (e.g. "Relt location" updated to "Relative Location")
-------------------------------------------------------------------------------------------------------------------
Overall: Setting up NanoLIMS was difficult and required contacting the authors. The lack of documentation makes
customization difficult. Although there are manuals describing how to work with the LIMS, there is no overall
explanation of the concepts that underlie NanoLIMS. This information is essential for the small lab starting with a LIMS
for the first time. The LIMS is designed for metagenomics sequencing and many screens, fields and default values are
specifically for that purpose, but it is never stated in the text. A lab that sequences solid tissue, biobanked samples or
blood would need to customize most of the interface, and the documentation is not complete enough easily do so.
NanoLIMS should either become more a more generic LIMS or declare itself as a metagenomic LIMS. Regardless, it
requires better documentation to support its claims of flexibility.
-------------------------------------------------------------------------------------------------------------------
Author response:
Scope of MetaLIMS (formerly NanoLIMS) redefined to be specifically for small metagenomics labs prior to input
into NGS sequencing pipelines and is now defined as such in the manuscript and in the GitHub wiki.
Figure added to GitHub indicating overall concepts underlying MetaLIMS for users new to LIMS
-------------------------------------------------------------------------------------------------------------------

MetaLIMS is a lightweight, easy-to-install LIMS system for smaller labs and facilities performing metagenomics studies. It claims to be easy to use and install and simple to configure. I reviewed the first version of this manuscript and found several concerns.

The revised manuscript has addressed all concerns to my satisfaction. MetaLIMS caters to metagenomics labs, an under-represented group in this field. The addition of allowing installation and use of AWS Lightsail as a hosting environment, as well as the overall improvements in documentation, installation, and clarity greatly support the aforementioned claims. It plays nicely with several versions of Genologics LIMS, the current commercial leader, and therefore MetaLIMS does not 'lock' users into it like other LIMS systems do. The authors also include a complete database ER diagram, which was appreciated (possibly not necessary for the publication itself, but definitely should feature in documentation).

The following suggestions are speaking from a slightly biased perspective as one of the developers on MISO LIMS, in table 1. for MISO LIMS, sample metadata can be added at any time, but is limited to pre-defined fields and free-form "notes"; input sample types can be configured through advanced computer skills to include any type of sample (for OICR this starts at 'Tissue'); for software, Eclipse is a development environment, not a deployment software; finally, the correct website is http://tgac.github.io/miso-lims/ .

I support publication of this manuscript.

Authors' response to reviews:

The authors have edited the information in Table 1 for MISO LIMS to correct information as suggested by reviewer-

-Sample metadata has been updated to 'Pre-defined fields and free-form "notes”. Sample type configuration for advanced users' -Eclipse has been removed for software -Website for MISO LIMS has been corrected with the given website (http://tgac.github.io/miso-lims/)