Macs in Chemistry

Insanely Great Science

eLabFTW

 

I just came across a new Electronic LabNotebook (ELN), eLabFTW is an open source solution powered by PHP/MySQL in Docker containers. One install can be for a team, or the whole institution. You can also install it on your computer for a personal notebook.

All the user needs is a web browser to access the notebook.

Upload any type of files, embed images in the text, Draw doodles directly with your mouse, Use templates for your experiments, Draw molecules with Chemdoodle, REST API for accessing programmatically your experiments, SAML2 authentication if you have an identity provider, Growing community of users and contributors scrutinizing the code and improving it, Highly customizable: you can change the colors, the status list, the items types list, etc. Can fit any kind of lab (chemistry, biology, physics, astronomy, etc.)

Full details are available here and there is a presentation here

There is also a demo account available https://demo.elabftw.net.


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Chemotion ELN: an Open Source electronic lab notebook for chemists in academia

 

A web-based chemistry ELN using the OpenBabel toolkit published recently https://doi.org/10.1186/s13321-017-0240-0DOI

The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user’s data but also in conventional external sources as provided by SciFinder and PubChem.

Project home page: https://github.com/ComPlat/chemotion_ELN

Developed/tested on Linux and Mac, deployed on Linux.

Other requirements: Modern internet browser supporting HTML5 and JavaScript. Recommended browsers: Chrome, Firefox (IE not supported).


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ELN training at Cambridge (UK)

 

Increasing numbers of electronic alternatives to the traditional paper lab book are available, offering advanced opportunities for managing your research. Hear from researchers and PIs across the disciplines who are using Electronic Lab Notebooks (ELNs) and those considering a trial, and from current providers.

The Office of Scholarly Communication provides a range of transferable skills and more specific research skills training. This training is tailored for researchers, however the courses are also open to:

All Graduate students in the University of Cambridge Librarians who are employees of the University and any of the Colleges Administrative staff who provide research support in the University

This event is sponsored by Dotmatics


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Findings Updated

 

The electronic LabNotebook Findings has been updated to version 1.4.2. There is a review of Findings here

bathy-nobubble@2x

Two new features:

  • Today' button in the experiment header to scroll to today, applicable to both the text view and the calendar view.
  • Special window for mailing list signup

Plus a host of bug fixes and improvements.


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BioBlocks:Programming protocols in biology made easier

 

The increased use of robotics and automation in experiments is rapidly developing field but coding the experiments can be a tedious and require expert programming knowledge. A recent publication “BioBlocks: Programming protocols in biology made easier” DOI describes a simple drag and drop web interface.

Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments.

bioblocks2

The Software, Tutorials and Code available on the webpage http://www.lia.upm.es/index.php/software/Bioblocks.


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Findings Updated

 

Findings 1.4 has been released. This sounds an important update to this popular electronic Lab notebook.

Better editor, better tables, better sharing, better protocols, better performance.

The full release notes are here


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SCINDR - The SCience INtroDuction Robot that will Connect Open Scientists

 

The SCINDR project aims to develop a way to connect, in real time, globally disparate researchers who are doing similar science so that they can work better and faster towards the development of new medicines

Once a researcher has their data stored on the ELN, or on any similar open database, for that matter, SCINDR would be able to detect if similar molecules, chemical reactions, biological assays or other features of importance in health research have been entered by someone else. If the robot identifies another scientist looking into similar features, it will suggest introducing the two to each other, so that they could start working together and combine their efforts and knowledge for the good of both science and the public.

SCINDR


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Findings Updated

 

Findings the electronic lab notebook for both MacOS and iOS has been updated.

Release Notes
Compatibility with the upcoming Findings for Mac 1.4.

Looks like there are more good things on the way!


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ICM-Scarab

 

Molsoft have just announced and interesting new product ICM-Scarab, a one-stop shop for capturing and analysing bioinformatics and chemoinformatics data. It provides and electronic notebook for storing experimental information integrated with query tools that allow the user to effortlessly search both internal and external SQL databases.

There is a webinar Wed, Jun 29, 2016 5:00 PM - 6:00 PM BST if you want to find out more.


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Findings Updated

 

I just noticed that the popular electronic laboratory notebook Findings has been updated.

Release Notes Version 1.3.4

  • Reduced CPU activity at app launch, in particular for large libraries.
  • Better responsiveness when typing in large documents.
  • Faster loading of large experiments or protocols, avoiding operations that could even lead to the dreaded spinning beach ball.
  • Automatic scrolling to the insertion point when pasting or when inserting various elements in experiments or protocols, like attachments, section titles, etc.
  • Superflous confusing newline after tables in experiments or protocols.
  • Automatic scrolling to the insertion point when typing was not always working.
  • Problems with some keyboard input methods (in particular Chinese: Pinyin) when used on a new empty line.
  • Document library path wrongly reset when Dropbox folder is in /Users/Shared.

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Bundle offer for Finding, Papers and more

 

There is an interesting bundle offer running at the moment.

"A collection of seven fantastic Mac apps to help you be more productive. Focused around writing, editing, researching and organising, these apps are the perfect companion to all researchers and scientists. The best part? This selection of Mac apps normally cost $305, but during this promotion (which won't last for long), the whole bundle is just $49.99!”

The apps are:-

Papers $80 Your personal library of research designed for your Mac. Papers ​is a multiple a​ward winning​ application developed for researchers. It turns your messy heap of PDFs into your personal library. It helps you collect, curate and stay up to date with your field.

Manuscripts $40 A writing tool like nothing you have seen before. Manuscripts is a writing tool for complex documents unlike any you have seen: it helps you with a complex writing project from outline to editing, proof reading and publishing stages, all within a beautiful Mac app.

Records $30 Records is a delightful and easy to use personal database. The perfect companion for everything you want to collect and organize in life, from your favorite movies to your customer invoices, offering a great balance between easy of use and powerful features.

Soulver $11 Soulver helps you work things out. It's more than a spreadsheet, and smarter than a calculator. Soulver helps you do quick calculations and work things out. Use Soulver to play around with numbers, do "back of the envelope" calculations, and solve day-to-day problems.

DEVONagent Pro $50 Your smart Internet (re)search assistant. DEVONagent Pro helps you search more efficiently on the web. It searches multiple sources, frees you from hunting for the really relevant results, and gives you power tools for your research.

TextSoap $45 Automate tedious text document cleaning. Automatically remove unwanted characters, fix messed up carriage returns, and pretty much anything else you can think. Stop manually fixing text documents and emails. TextSoap can automate away that tediousness.

Findings $49 Your research notebook, reinvented.

All 7 applications for $49.99


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Electronic Lab Notebooks for iOS

 

I've just finished updating the Mobile Science site there are now over 400 entries covering all areas of science. The latest entry is Notelus an electronic lab notebook (ELN). ELNs seem to be increasingly popular, and having access to your notebook on a mobile device that you can carry into the lab/library etc. is very attractive.

There are a selection of ELNs for iOS, some also have desktop versions, whilst there are other systems that are web-based and can be accessed from most devices.


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Findings LabNotebook Updated

 

New in version 1.3 of Findings

  • Support for iPad.
  • Support for landscape orientation on all iOS devices, & improved layout for all screen sizes.
  • Support for iOS 9 multitasking enhancements for iPad (Split Screen and Slide Over).
  • Export Findings archive via the Share button.
  • Import of Findings archive from other applications (Mail, iCloud Drive, Dropbox, etc.). Like on Mac, you can select which document to add or merge.
  • Significant improvements to the protocol browser (p<0.001): relevant science fields and separation of your protocols, protocols from others and Findings example.
  • Create a new experiment directly from a protocol
  • Support for 3D Touch on application icon, with shortcut items to show your experiments, the protocol browser, or a new experiment.

We also improved a lot of things in version 1.3:

  • Clearer requests to enable notifications (for timers).
  • Nicer-looking superscript & subscript.
  • Easier selection of subfield in protocol metadata editor.
  • Message to the user when an attachment does not support Quicklook & cannot be previewed on iOS.
  • More options for troubleshooting sync under the 'Advanced' section in the settings, including manual sync trigger, Dropbox cache reset, Dropbox file removal, and sync diagnostic logs.
  • Completed experiments are automatically marked as ongoing when adding new content for current or future days.
  • Example protocols that come with the app are now read-only.
  • Tweaks to the app icons, in particular adding missing assets for 3x resolution on iPhone 6S+.
  • Allows navigation back to last day of an experiment after moving to today, by having the 'Today' button become 'Last Edit'.
  • Creating a new experiment uses a clearer 'Create' button instead of the potentially confusing 'Save'.
  • Experiment and protocol deletion now possible in the metadata editor ('i' button).
  • Protocol creation possible from any screen of the protocol browser (previously, it was only possible from within a subfield).
  • Sharing via AirDrop.
  • Full-fledge protocol browser to select a protocol to add to an experiment.
  • Watch: start countdown timer immediately when adding via the Watch app.
  • Watch: dismissing iPhone alert when timer is stopped on Watch app.
  • Watch: clearer accessibility labels on Watch app.

We also fixed a lot of small annoyances and bugs:

  • Hiding the irrelevant calendar icon when editing protocols.
  • Table display bugs and truncation in document view.
  • List numbering wrongly interrupted by table.
  • Update completed state of paragraphs after reordering.
  • Actually query start date when duplicating an experiment.
  • Correctly displaying experiments pending completion under the 'Ongoing' tab when selecting an experiment to duplicate.
  • Missing information in diagnostic section of pre-filled feedback emails.
  • Using the correct tint color in the various protocol-related views.
  • Insertion of picture below selected paragraph when using the paragraph toolbar.
  • Keyboard hiding modal menu for changing note type.
  • Extraneous space in support button.
  • Removing unused options wrongly displayed for Findings in the Settings app.
  • Icon missing or incorrect icon when using swipe-to-right to toggle the completion state of a paragraph in the experiment editor.
  • Displaying multi-line text in the metadata editor screen.
  • For a paragraph added on Mac, a timer could only be added after "deleting" a (non-existing) timer.
  • Attachments not duplicated when duplicating an experiment.
  • Correctly displaying styled text (bold, italics, etc.) in bullet-list paragraphs.
  • Watch: unreliable notification when starting timer from Watch app.
  • Watch: glance update after updating experiment progress or timer in the Watch app.

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Findings Updated

 

The popular electronic notebook Findings has been updated.

Release notes are here

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Findings Updated

 

Findings is an electronic notebook for scientists.

The main new features are:

  • Much improved export, with options to export multiple experiments based on projects and dates, and many more options for PDF output (and print).
  • A brand new archive format to export and import experiments and protocols, which makes it very easy to share documents and collaborate on their content. One subtle but powerful feature is that re-importing an experiment or protocol will not create a duplicate, but will instead merge the latest changes. This means collaborators can keep sending new versions of a document to each other, and it will magically update their library.
  • Full-text search across all experiments (or protocols).
  • Search within a document, with proper highlighting and keyboard-based navigation through the search matches.
  • Much nicer experiment cards, in particular using a vignette thumbnail, showing a project color, and with the calendar strip functioning as a progress bar for multi-day experiments.
  • In addition to the free Basic version, new unregistered users are now also offered a 30-day trial of the Pro version;for 30 days, the 20-day experiment limit is thus lifted.

There are also tons of improvements and bug fixes.

Collaboration also got better, you can also export experiments as archives, that anybody can read with the free Basic version of Findings.

There has also been some changes to the pricing structure, the basic individual version is free but there are discounts for group (5) purchases, and it sounds like if you have a bigger group it would be worth contacting them directly because larger discounts are available.

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Mbook

 

Mbook is an Electronic Lab Notebook designed by chemists for chemists, it is a cloud based solution focused on the needs of synthetic chemists. Runs on any web browser and therefore requires no application installation or updates. Zero footprint and always updated. Immediately scalable, you can grow your number of users without having to change infrastructure or installations.

Experimental elements:

  • Reaction scheme and experimental conditions
  • Stoichiometry table and experiment write-up area
  • Analytical data (NMR, MS, etc.) for reactants, solvents and products
  • MSDS datasheets for all experiment participants
  • Literature references and other relevant documents
  • Image files (product appearance, TLC, etc.)

It comes in various favours from a basic setup to an expert suite, the difference being the number of different spectroscopy plugins that are included.

There is an online guide and a test drive version.

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Shazino software

 

I recently became aware of a new company specialising in software for scientists Shazino have developed a number of interesting applications for both Mac OS X and iOS.

The best known app is PaperShip an iPad, iPhone, and Mac application designed to help you keep your articles organized with your Mendeley or Zotero library. However they also provide a couple of smaller apps that make life easier in the lab.

Laboratory Timer, Fast Counter and SciKey a scientific keyboard.

The latest addition is an electronic labNotebook called Hivebench, this is available for both MacOSX and iOS. Looking at the website it seems to be aimed at molecular biologists/biochemists, and there is a free version that allows unto 10 scientists to collaborate.

mobile_devices_hero-a3f5971a11bba4791e0b09df3e8a5993

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Findings and SZMAP updated

 

Findings 1.2.3 the electronic notebook has just been released. Already using Findings? Menu Findings Check for updates...

OpenEye have just announced the release of SZMAP v1.2.1. This is a critical upgrade that fixes several bugs.

  • The Water Orientation VIDA Extension now saves orientation probability data and ensemble energy, vdw and order data on probe molecules as SDData. When probes generated by this extension are written to an .sdf file, these values will be written as well.
  • The Water Orientation VIDA Extension (version 1.1.3) now displays the correct water orientations for results from szmap version 1.2.0. It is also more compatible with 2D depictions in the 3D display.
  • gameplan no longer crashes when all stabilization test sites clash.
  • pch option -nonsymmetrized_charges now works to control AM1BCC partial charges. The default has been changed to true so as not to alter the default behavior.
  • pch no longer treats CYS residues bonded through the sidechain to a non-CYS as anionic.
  • pch no longer duplicates non-standard groups containing a metal (such as cofactors) and groups they are bonded to.
  • The hydrogen charge on the standard water probe is now correctly listed as +0.327 not +0.237 in SZMAP Theory.
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Findings Electronic Lab Notebook

 

I just noticed that Findings have altered their pricing structure, you can now download a free version that contains all the functionality of the full version but is limited to 20 experiments.

Findings Basic is the entry point for users that have limited needs, or newcomers that just want to try things out. With Findings Basic, you can create up to 20 experiments. The entire app is otherwise fully functional, including export and sync, and you can create and edit an unlimited number of protocols.

There is a review of Findings here

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Findings LabNotebook Updated

 

The electronic lab notebook Findings has been updated to version 1.2.

Probably the big new feature is the ability to add tables to experiments, I'm sure this was a much requested feature. Also interesting to see the added areas of science, sounds like the user base is diversifying ;-)<

New Features:-

  • New: tables in experiments and protocols. Insertion of new tables can be done using the corresponding menu item in the Format menu or the table icon in the top toolbar of a document. After creation, the cells can be navigated using the tab and shift-tab keys. For insertion/deletion of columns and rows, use the corresponding menu items in the Format menu.
  • New: countdown timers. Timers can be created for any paragraph in an experiment or a protocol by clicking on the timer button in the gutter of the text view. Findings sets the duration based on the content of the paragraph, but it can also be adjusted manually using the 'gears' button. Timers can be started, paused or stopped from the text view of the experiment, from the experiment card, or from the timer panel (via the Window menu). Local notifications will be displayed when the timer is done.
  • New: timestamps. A timestamp can be created for any paragraph in an experiment and will by default indicate the time at which it was created (it can be edited as needed to change the time).
  • New: stopwatches. Clicking a timestamp will change it into a stopwatch, showing the time elapsed since the timestamp. It can be stopped to record the end time as well.
  • New: field for 'Computer Science', subfield 'Microfabrication' in Engineering, subfield 'Proteomics'. Let us know if you have more requests for missing fields or subfields.

There are also a number of improvements and bug fixes

These features have also been added to Findings for iOS.

There is a review of Findings here.

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Findings Updated

 

The electronic lab notebook Findings for Mac has been updated, this free update includes a new table layout feature, and timers and timestamps. It also includes a couple of bug fixes. The iOS version has also been updated and there is now also a Findings app for the Apple watch. So if you were looking for an excuse to buy a new Apple watch this seems like the ideal reason!

There is a review of an earlier version of Findings here.

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ChemStack

 

ChemStack is a collection of components that allow users to build chemically intelligent systems, such as collaboration tools, information portals, electronic laboratory notebooks, eLearning systems etc.

Some examples of useful chemical interfaces include:

  • A sketcher to draw molecules
  • Viewers to display molecules
  • Components to display and interact with spectra
  • 3D graphics engines to investigate 3D structures
  • Text based input for IUPAC names and queries

There is a demo here that searches the ChEMBL database of 1.5M structures.

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Findings Updated

 

The Electronic LabNotebook Findings has been updated

1.1.1, build 2396,
New psychology field, subscription to beta updates, and small fixes and improvements.
Release notes for version 1.1.1:
New: psychology field and subfields in the protocol library, as well as additional subcategories for the cookery "field".
New: subscription to pre-release versions of Findings. To be notified of beta versions, check the corresponding box in Preferences > Options.
Improvement: multiple spaces can be inserted, instead of being collapsed into one.
Improvement: native full-screen window button in Yosemite.
Improvement: displaying the year for dates outside the current year in the experiment cards.
Fix: typing composed characters using special keyboard input (Japanese, Korean, Chinese, etc) could lead to extra "fantom" characters.
Fix: undo not working when deleting an attachment while the selection includes part of the legend.
Fix: now showing styled text for the next task in experiment cards, instead of exposing the ugly and confusing markup.
Fix: experiment cards scrolling area not properly aligned with the window borders.
Fix: removing unused menu items that would only lead to confusion.
Fix: unsightly baseline changes when applying subscript or superscript.
Fix: the window would sometimes remain blank after exiting the welcome guide or the store.
Fix: rare issue where Dropbox sync could not be started because of an attachment with an extension starting with 'fd'.
Fix: library would not load when using Dropbox and the OS X account name is different from the home folder name.

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Findings LabNotebook

 

Findings LabNotebook for iOS has been released. This comes with Dropbox sync.

screenshot-progress-ios

There is a review of the MacOSX version here.

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Findings Lab Notebook

 

Findings is a Mac electronic lab notebook designed for scientists that aims to replace the paper lab notebook still in use in most research labs. I did have a look at Findings when it came out but it did not seem well suited to a chemist so I thought I’d wait and see what the reaction was from other disciplines. Findings app has very distinguished roots, it was founded by Alexander Griekspoor (author of the Apple design award winning Papers and EnzymeX) and Charles Parnot (of Xgrid@Stanford fame), an ex-scientist metamorphosed into a software developer.

A reader sent me this initial view of Findings and I thought I’d share it since it nicely showcases the application:

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Green Lab Notebook

 

Molecular Materials Informatics, Inc. have been updating and expanding their portfolio of iOS apps, the latest addition is Green Lab Notebook, this looks like an interesting application for managing chemical reactions on a handheld device.

There are now nearly 350 mobile science apps on the Mobile Science website.

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Findings LabNotebook

 

The developers of Findings are looking for people to test the latest features.

Findings Sync can already be enabled in the version 1.0.6 of Findings for Mac. First, make sure you have the latest version using the menu Findings > Check for Updates. After restarting the app, you can enable Dropbox sync in the 'Library' tab in your preferences (accessed via the menu Findings). Note that because of OS X security, you will need to give access to your Dropbox folder by selecting its location on disk (typically the Dropbox folder in your home folder). Do the same on all your Macs, and have all your experiments and protocols in Dropbox, available everywhere! Please let us know if you have any question or problem: send us an email using the Help menu in Findings

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Findings Update

 

The electronic notebook Findings has been updated

1.0.5, build 2264
New: display completed experiment as a list
Release notes for version 1.0.5:
New: display experiment as a list (menu Findings > Preferences > General).
Improvement: file preview update when modified externally (for instance after updating an Excel file).
Improvement: day editing and insertion of a day before the first day.
Bug fix: high CPU usage and memory build-up triggered when adding a present or future date to an experiment previously marked as completed.
Bug fix: parts of an experiment could have a wrong completion status (wrongly grayed out).
Bug fix: PDF export menu stays disabled after canceling.
Bug fix: memory leak in PDF export.
Bug fix: inconsistent button labels in embedded license store.

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Core ELN (Electronic Lab Notebook) Chemistry application

 

Core Informatics have announced the release of it’s new chemistry app for Platform for Science. The newly developed Core ELN (Electronic Lab Notebook) Chemistry application is designed to help chemists document research activities and compound registration in the cloud.

The Core ELN Chemistry app, developed through a partnership with ChemAxon, streamlines daily documentation responsibilities of research chemists across all R&D disciplines including analytical, medicinal, process, & CRO. It provides a chemically intelligent and flexible environment which allows scientists to manage synthetic transformations, capture experimental details and analytical results supporting internal and contract syntheses.  Compound registration is augmented by powerful search capabilities that span reagents, compounds, experiments, instruments, collaborators, and synthetic campaigns.

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The electronic LabNotebook app Findings has been updated

 

Findings 1.0.4 is out!

New: ongoing/completed state of experiments, experiment vignette, and other improvements

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Labarchives

 

I was recently sent details of another electronic lab notebook (ELN), Labarchives appears to be a web-based system that supports all major platforms any time you are connected to the Internet. This includes any Windows, Mac, or Linux system using Internet Explorer, Firefox, Chrome, and Safari, as well as on the iPad.

The Professional version is priced for academic institutions and non-profits at $99 per user per year (which includes 100 GB of storage per user), representing a 50% discount off of pricing for commercial organisations.

Special departmental and site license pricing is also available as well as quantity discounts.

LabArchives can also be installed on a local server.

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