E-WorkBook Chemistry blog

Saving time when writing procedures

September, 2016, Nathalie Batoux

Historically, when synthetic chemists worked in paper notebooks, entire experiments or parts of procedures would often be repeated. Even for new reactions, the procedures of aqueous workup and purification were often similar. Consequently, a significant amount of time in the write-up of an experiment was spent transcribing existing methods and protocols.

Moving into the digital age, it’s possible to get around the tediousness of re-entering existing data, and, although ‘copy and paste’ operations are a great help, they can be a bit cumbersome as you need to know where the block of text already exists.

In the IDBS E-WorkBook for Chemistry ELN, we are striving to develop tools that make the life of the synthetic chemist easier. In a previous blog (Procedure write-up and data integrity, June 2016), we described the ability to directly and synchronously reference the components of a stoichiometry table in the procedure write-up. Following on from this, we have now added the capability for a user to define their own custom text phrases, which can be added to the procedure at the click of a button.

Procedure write up NB Sept 2016
Making the text phrases easy to define and local to use will help ensure that experiments are written to a better quality and standard, helping with reproducibility and in the capture of knowledge.

 

Bringing back additional information about a 'looked-up' structure

August, 2016, Anthony Barnardo

The ability to reference chemical structures and associated data from a third-party source is an essential feature of any chemistry ELN. No one wants to have to go to a paper catalog or open a separate system to search for the properties of a compound when you’re planning a synthetic reaction. With the E-WorkBook Chemistry ELN, we’re making this process easier to ensure we get the best blend of functionality and performance for the chemist using the software.

In a previous post (‘Adding Reagents Simply’, June 2016), Virendra Mishra introduced the new look-up functionality, to allow for the connection of disparate information sources into the ELN environment. We’ve now extended that functionality to allow the chemist to view the structure of the reagent and the associated information within the stoichiometry table itself by clicking on the information ‘i’ button in the relevant row.

Chemistry blog Aug i Button

By providing easy access to the associated information such as compound ID’s, batch and supplier information and hazard metadata, the chemist can be properly informed – not only when the reaction is initially performed, but when it may be repeated by someone else.

How concentrated do you want your reaction to be?

August, 2016, Nathalie Batoux

Since the release of the E-WorkBook 10.1.2 Chemistry ELN, we have been busy augmenting the core features of the stoichiometry table. One of the enhancements we have recently implemented is the calculations of solvent concentration, with the ability to determine the molarity but also the solvent volumes of a reaction. Whilst molarity is an easily understood concept, the solvent volume measure provides an easier ratio of the quantity of solvent required per gram of reagent, which is a useful factor to consider when scaling a reaction.

Solvent chemistry blog NB Aug 2016

Concentration is an important factor in a synthetic reaction, as it not only directly affects the rate of the reaction, but also the formation of impurities and side-products. Many discovery chemists typically run more dilute reactions to achieve a cleaner end result. Conversely, a process chemist may deliberately run the reaction in a more concentrated solution because of the practical size of equipment required. This also forces the formation of impurities to determine an appropriate purification strategy.

We believe this additional data will help to improve the reproducibility of experiments and to ensure that experiments scale with the desired outcome.

Special symbols in procedure write-up

August, 2016, Anthony Barnardo

Chemists commonly need to use non-standard characters during procedure write-up, which may include Greek characters in chemical names and ‘as’ symbols for reaction conditions. Many text editors support these but the functionality is often hidden away, requiring the use to change the font type to ‘Symbol’ font and look for an individual character, or try to remember some arcane combination of Alt keys and digits to access their desired ASCII symbol.

Chemistry blog Aug Symbol insert

In the E-WorkBook for Chemistry ELN, we wanted to make use of symbols easily accessible, so that a user can quickly insert these into a procedure write-up, simply by clicking on the required symbol. The symbol icons are conveniently sized and spaced, facilitating use of these on tablets as easily as on a desktop PC, making it easy to complete your write-up in the lab or back at your desk.

The Chemistry ELN is here!

July, 2016, Ian Peirson

We’re very pleased to announce that the Chemistry ELN has been released with v10.1.2 of E-WorkBook in July.

Considering we started from just design documents in January, the chemistry development team has worked hard to provide the user with a fully-functioning stoichiometry engine, which is linked to the semi-automated procedure write-up. This functionality is enhanced by providing standardized interfaces to registration and inventory lookup sources, to make the process of inputting and exchanging data with other systems a lot easier.

It's worth mentioning that we have developed this in conjunction with our customers in the USA and EU, and I’d like to thank them for giving us constructive feedback to help shape the design of the product. This v10.1.2 release provides a good foundation for us to further build upon, and to enhance the capability of the product, and we are already planning the next stages of development to support releases in September and December. As always, the team will be blogging throughout the development, so don’t forget to bookmark this page to keep up to date with our progress! If you’re interested in contributing ideas to our forum discussions, please get in touch by emailing info@idbs.com.

Stoichiometry data and structure edits

June, 2016, Anthony Barnardo

Sometimes, when writing up a synthetic chemical reaction in your notebook, you might need to go back and update the chemical structures that were originally drawn - perhaps because of some small error such as forgetting to add an atom label, or because you were better able to elucidate a molecular structure after analysis.

In E-WorkBook Chemistry ELN, we have developed our stoichiometry item panel to cope with just such scenarios, to allow the original reaction scheme to be edited and updated, and for all associated  experimental values e.g. mass or volume quantities to be retained.

After the structures have been edited, the system will automatically perform all stoichiometric calculations again, as a change in structure may involve a change to the reaction component’s molecular weight and hence the number of moles available to the reaction. This in turn may have an affect on the theoretical quantity of product and the associated yield. All updated calculations appear automatically within the procedure write-up section as well as the chemistry stoichiometry table itself.

Adding reagents simply

June, 2016, Virendra Mishra

It is often very time consuming to draw molecules for well-known reagents, but often the chemical structure is needed to derive the molecular mass for stoichiometric calculations. Also, a chemist might sometimes scan barcoded containers from their inventory system to bring in starting materials.

VM blog 1 - lookup

The E-WorkBook Chemistry ELN now includes a chemical lookup functionality to associate chemical data from other internal inventory system or external applications. This chemical data could comprise of the chemical structure, molecular mass and formula, but other associated quantifier data such as concentration or density, or supplier information is also of value.

The simplest way to search is to perform a text query, either by synonym or partial IUPAC name. When the hit is identified, the user can add it to the stoichiometry table as a new component, with the ability to define the role of the component i.e. reactant, reagent, solvent etc.

This interface to inventory within the chemistry ELN product is very configurable and allows the user to define multiple sources, which can be searched simultaneously. The supported integration mechanisms include web services to online or local systems, database tables and parsing of flat files e.g. CSV/SDF. By providing access to multiple sources, the chemist is able to quickly and easily add reagents to their planned synthetic reaction.

Procedure write-up and data integrity

June, 2016, Anthony Barnardo

Earlier this month I wrote about the auto-text feature we provide in E-WorkBook Web for chemists, which allows you to add predefined phrases to the procedure write-up with a single click. These phrases consist of the names and quantities you have previously entered into the stoichiometry table (see the “Making write-up simple” post).

This functionality is now even more powerful!

9 - AB writeup

Now, values are kept in sync between the stoichiometry table and the procedure write-up. Imagine writing up your procedure, adding reaction component names and quantities using the one-click auto-text feature. Later on, you realise you need to make an adjustment to the scale of the components in the stoichiometry table. You don’t need to rewrite the procedure – the system will automatically update the corresponding quantities in the procedure write-up for you.

Not only does this save you time, it also ensures greater data integrity, leaving you time to focus on what matters to you – the experiment itself.

Round and round, I calculate

June, 2016, Nathalie Batoux

Traditionally, when you needed to work out the quantities of reagents required for a synthetic reaction, your best ally used to be a piece of paper, your calculator and your integral knowledge of the formulae for calculating the required quantities. Many common reagents are often liquids e.g. Et3N with a density of 0.79 g/ml or pre-packaged solutions e.g. 1M BuLi in THF, thus requiring concurrent density and concentration calculations.

8 - NB Stoichiometry

Using the new E-WorkBook Chemistry product, we have translated the thought-process of the chemist into the software, and designed our performant stoichiometry calculation engine to handle all the calculations in one go, allowing you to calculate and record all the amounts in your reaction from the starting materials, reagents and the final calculation of the yield once you have purified your product.

In addition, the system also handles the "reverse" calculation e.g. “I’ve done this reaction before, and I know it gives me a 75% yield after purification. If I needed 5g of product, what quantities of reagents would I need?”. By providing the system with the equivalent scale of the reaction components, and the desired amount of product and the expected yield, it will work backwards to give you the required amounts of all the starting material, in a single click.

With the E-WorkBook chemistry product, your old calculator will start to gather dust…

Making reaction data entry more manageable

May, 2016, Anthony Barnardo

As a synthetic chemist, when you are recording your experimental data in a notebook, there are multiple data elements to account for each reacting component i.e. chemical name, molecular formula, molecular weight, mass or volume, number of moles, number of equivalents, whether the reactant is ‘limiting’ in the reaction, and so on.

chemistry blog post may 23 b

To help users focus on what they need, it is challenging to establish the right balance in the interface between showing enough information at once, or showing too much.

The new stoichiometry experiment item of the E-WorkBook chemistry ELN makes this easy, by providing two modes for each reaction component row in the stoichiometry table – view and edit. You can open an expanded ‘edit’ mode for an individual row, whilst still being able to see the relevant data in the other rows, which remain in ‘view’ mode.

When considering the usability of an electronic lab notebook (ELN), we find it’s often these little details which count. They may seem minor at first, but taken together, they all contribute towards our goal of making E-WorkBook web the most user-friendly chemistry ELN available.

Making write-up simple

May, 2016, Anthony Barnardo

One of the things that all of our chemistry customers seem to agree on is the utility and value of the auto-text features that we provided in the desktop version of our E-WorkBook chemistry ELN, for assistance in the writing up of experiments.

chemistry blog post may 23 a

It can be time-consuming for chemists to manually copy across reagent names and numerical quantities from the stoichiometry table to the procedure write-up, and this can lead to transcription errors. However, it is crucial that the procedure write-up is completely accurate and reliable, as it could form part of a future patent submission.

To help chemists, we thought it was essential to provide auto-text support for procedure write-up in the new web-enabled chemistry ELN. In the new product, with a single click, users can easily add predefined phrases to the procedure write-up, consisting of the name and quantities the user has previously entered into the stoichiometry table. It’s another IDBS feature that makes the job of the chemist that much easier and more accurate!

Partnering with ChemAxon: What does it mean to IDBS

May, 2016, Nathalie Batoux

chemaxonHistorically, IDBS developed its own chemistry technology internally, which was successfully used to support our E-WorkBook chemistry ELN and ActivityBase screening platform. When transitioning to the web, we reviewed our approach and chose to partner with ChemAxon, who were able to provide us with an easy-to-use solution for web chemistry. This technology included the web drawing tool Marvin JS and the indexing service JChem.

Collaboration with ChemAxon is not new to us – in the E-WorkBook desktop electronic laboratory notebook product, we already leveraged the Reactor technology for enumeration of parallel synthesis, and calculator plugins for physicochemical property and IUPAC nomenclature predictions.

To promote our strategic partnership, our chemistry product management team regularly visit the ChemAxon team in Budapest, where we have face-to-face discussions to investigate each other’s product roadmaps and requirements, doing deep-dives into technical details for APIs and web services to faciliate integration. In addition to this, we have a regular biweekly catch up where both teams can discuss progress and key dependencies.

So, is this partnership working? Absolutely! Whilst ChemAxon teams concentrate on structure drawing, rendering and storage of chemical structures and reactions, at IDBS we are able to focus on bringing these technologies to the foreground through the E-WorkBook chemistry informatics tools and workflows to support organic chemists in discovery chemistry, process chemistry and industrial research.

This partnership is continually evolving, as ChemAxon have many valuable tools that we think will be beneficial to our customers. As an example, we are currently looking at close integration between our new web-enabled chemistry ELN and ChemAxon’s chemical compound registration tool, to provide a complete workflow to our customers.

Chemically intelligent stoichiometry

May, 2016, Anthony Barnardo

One of the many benefits of integrating ChemAxon’s Marvin JS and JChem web services technology into E-WorkBook is the speed with which we can develop new electronic laboratory notebook solutions which have chemical intelligence built in – taking our chemistry ELN to the next level.

chemistry blog post 4

Take, for example, the new stoichiometry functionality of our chemisrty ELN (scheduled for release in E-WorkBook 10.1.2). When you draw a chemical reaction in an electronic notebook experiment item, our software seamlessly uses the ChemAxon technology to identify which of the reaction’s chemical structures are reactants, which are agents, and which are products. The E-WorkBook chemistry ELN then automatically generates the stoichiometry table with the various components located in the correct dedicated sections. You can intervene if you wish to change the type of the components in the table, or further refine them - such as when you need to mark one agent as a catalyst, and another as a solvent.

This is valuable because you often need to record different kinds of properties, and perform different calculations, depending on the component’s type. For example, for a solvent you may need to record its volume, whereas for a catalyst you may need to use fractional equivalents without limiting the equivalents of the expected product.

Structuring these kinds of reaction semantics into your chemical experiments has never been easier, with ChemAxon’s world-class chemical intelligence working for you inside the best chemically enabled ELN on the market – E-WorkBook Web.

Chemistry Forums: involving customers in our development

May, 2016, Nathalie Batoux

When we started working on the E-WorkBook project for bringing chemistry notebook functionalities to the web, it was clear to us that we wanted it to be a tool that would be useful and intuitive to chemists - something that they actually wanted to use.

Many of us in the team have years of experience in the lab, so we have a good grasp of what this is all about...but, we wanted to ensure that our ideas were aligned with the expectations of our customers. And, what better way to check this than talking directly to our customers? So we did and set up the IDBS Chemistry Forums to meet quarterly, both in Europe (Munich, Germany) and in the US in Boston.

At each meeting, we present ideas for the electronic laboratory notebook, propose design for specific chemistry functionalities, examine workflows of organic chemists and demo live software straight from our development portal.

We are seeing direct benefits of this approach:

  • Immediate feedback on the recently developed software: if something needs modification this can be done very easily before we are too far down the line. Our development team is working in an Agile manner, allowing quick adaptation to changes.
  • Prioritization of the functionalities at a more granular level. We have been able to discuss the relative priorities of functionalities so we can focus our development and testing effort to get the most useful features first.
  • Analysis of what differs from one company to another but also from one type of chemist to another. This allows us to have a better sense of priority for what to plan in the next development phase.

From the customers’ perspective, the benefits are evident - not only are they empowered and can actively participate in the development of the product, but they also have direct visibility of our progress which helps them with deployment planning. ChemAxon (our strategic chemistry partner) also attends these events, which gives them visibility of customer needs in different areas.

It’s an excellent way of involving everybody in designing great software that people want to use.

Quicker, faster structure drawing

May, 2016, Anthony Barnardo

chemistry blog post 2

Industry is moving away from traditional heavyweight desktop solutions (with all the support and maintenance overhead they entail), towards more lightweight, web-based solutions. ChemAxon’s Marvin JS (JavaScript) chemical structure editor, used directly in the E-WorkBook chemistry ELN, provides the ability to draw and edit chemical molecules and reactions, without requiring the user to “hotlink” out to installed client drawing packages. This streamlines workflows for end-users by saving on button clicks and application load times, and reduces total cost of ownership for IT managers by saving on the licensing fees for additional applications.

MarvinJS also allows our customers to leverage more complex molecule rendering, such as complex organometallics and polymer structures. This integration to ChemAxon’s technology means that we can receive regular updates (benefiting from any new changes) and that the IDBS development team can focus on the core functionality of the product.

A new start for E-WorkBook Chemistry ELN

May, 2016, Ian Peirson

Our chemistry ELN is getting a new look and feel! As part of the transition of functionality to the web-based E-WorkBook client, we’re completely re-designing the user interface to make it simpler and easier to use for chemists.

Chemistry blog 2016

A strategic partnership with ChemAxon (www.chemaxon.com) has allowed us to rapidly establish a web-based cheminformatics platform, providing the basis for our next-generation chemistry ELN product. In addition to implementing the MarvinJS and JChem tool from ChemAxon (check out the video on YouTube here), we’re leveraging a lot of the deep-knowledge and experience from our legacy E-WorkBook desktop chemistry electronic notebook platform.

There’s a lot of legacy chemistry functionality to migrate to the web during our application rebuild, but we’re making good progress. However, instead of conducting this development process in a silo, we’re actively working with interested customers. IDBS run Chemistry Forum events in Boston and Munich every three months, to empower users and allow them to help shape the product. These round table discussions have yielded great insights and helped to set the vision of where we want to take the E-WorkBook Chemistry ELN.

Chemistry is alive in E-WorkBook and you can bookmark this blog to keep up to date with our development. There are lots of interesting things to look forward to!