Education

CULGI is a great aid in teaching chemistry at both the undergraduate and graduate level, to satisfy the needs of the teacher and student in the 21st century. According to the World Economic Forum, digitalization of Research and Development in the chemical industry leads to a new market of more than 25 billion USD by 2025. Companies, such as BASF, are taking the lead in defining new ways of interaction between researchers.

While the industry is changing rapidly, the question now is: how do we teach our students about the revolution in digitalization? Students use internet, computers, smartphones and social media all the time: it is part of their everyday life.  At the university, we are perhaps still struggling with age-old paradigms for teaching new insights, often still by hard-copy books, hand-written exercises and in a classroom where the teacher needs to convince students that chemistry is exciting and modern while writing structures on a blackboard (or whiteboard).

CULGI has always had the belief that scripted workflows, in combination with a vast modeling library, could assist both teacher and student in grasping concepts more quickly and more effectively, by hands-on access to the latest tools in computational chemistry. Imagine that an undergraduate can operate the same professional software as a researcher in a state-of-the-art pharmaceutical company.

Please check out the solutions below how we achieve that. For professors that have bought a research license of CULGI, all licenses for teaching are free, including free licenses for home PC’s of students.

Try Culgi for free

If you are an academic from a government sponsored research institute or university, you are eligible for a free trial license. License for students in class is free, also for home PC.

Notice that we only accept requests from tenured professionals.

If you are a student or post-doc, consult with your supervisor.

13 + 10 =

The PREAMBLE

Moving away from the blackboard is not easy, for lots of reasons. For example, when we start using a modeling software in class, suddenly several issues pop up that have nothing to do with teaching, but with the organization of IT infrastructure and licenses. For example, how do we make sure students have the right license? Well, with CULGI this problem is solved: all students in the class have a free license, that they can use on their own computer (laptop, PC) for the practical course and take-home exercises. CULGI installs just as easily on a cluster or network. There is no issue with network-based licenses or other cumbersome licensing systems. As long as the professor has bought a research license, all teaching licenses are free, and the license file is simply co-installed with the software. 

A teaching license is for a fully functional package. If the student PC has parallel processing: please use that. If there is a IT infrastructure for connecting to a large supercomputer somewhere on- or off-campus, one can use the software in client-server mode, although this should be reserved for advanced classes). 

 

Step ONE: Workflows

Typically, undergraduate chemistry students have not been exposed to programming before. While in a traditional curriculum this is not a problem, one needs to anticipate the modern digitalization of chemical R&D, which is full of workflows and programming. Our CULGI Graphical Programming Environment is an excellent tool to learn the first steps in programming, while from the beginning working on a significant chemical problem. The course starts from a humble beginning that includes teaching the distinction between hardware and software, to the first steps in writing a series of commands in a workflow, until they can make a 30-40 line workflow for building a lipids bilayer.

CULGI script is a meta-language, with simple syntax and commands suitable for chemistry. The organization is through objects (molecules, calculation methods, etc.), with properties. A very sophisticated aspect is that students do not need to type in commands explicitly, but instead drag-and-drop commands to a central canvas. In addition, the interface is intelligent enough to capture logical errors interactively. Help is integrated with the software.

Step two: Make it Your Own

Instead of a pre-determined one-possible-answer hand-written exercise, as typical in old-style-curriculum, the students develop an electronic workflow as their own individual solution to a challenge. As a result, students have the feeling, sometimes for the first time in their career, that they have created something that is their own.

We have found this aspect the most valuable part of teaching through workflows. Instead of top-down imposing, the student learns bottom-up, and will not forget quickly what new concepts he or she has learned.

The enclosed workflow is a few ten lines for making a lipid bilayer. Undergraduate students learn to make the script in six sessions of each one day. The calculation takes ten minutes on a common PC, more than fast enough for a task in a practical course or home-exercise.

As the course advances, students learn to think about chemistry (what if one adds lipids with three tails?), theory and algorithms (can one write a script that speeds up the bilayer formation?), visualisation (how to make it really nice), and biology (what would happen if one adds proteins). 

 

Step three: Increase complexity

In a traditional undergraduate theoretical curriculum, courses quickly specialize in a plethora of topics, such as statistical thermodynamics (physics and chemistry departments), quantum chemistry and molecular modeling (chemistry), chemical informatics (pharmaceutical department), thermodynamics (chemical engineering), and so forth. But real research in industry is about integration and collaboration, not about the dissection of methods. The artificial division is also no longer necessary. CULGI includes all modern computational chemistry. In a single undergraduate course, the student could just as easily write a workflow for calculation of molecular orbitals, a workflow for molecular modeling, chemical QSAR, or engineering thermodynamics; or any a combination thereof.

The depicted example is from our Automated Fragmentation and Parameterization Scripts, which handle all scales simultaneously. The script is perhaps too difficult for undergraduates but easy enough for graduates and post-docs. Such advanced workflow can contain hundreds of lines of code. The scripts are also available in python, as shown.

STEP FOUR: EXERCISE and EXAM

In old-style curriculum, in a theory class, a teacher poses a set of questions, and a student returns hand-written answers, as home-exercise and also at the exam.

In the new-style scripted workflow class, the student develops a workflow as a small CULGI script, that is validated by the teacher on logic and outcome.

Moreover, CULGI is easy to install, and for students working at home, free. This means that students can also do their home-exercises at their own pace, and simply send the workflow electronically to the teacher for review.

We have found that students quickly get addicted to writing workflows. They are proud to find original solutions, and they really enjoy being part of a professional community.

 

And further: Data, data, data

The digitalization of chemistry includes many more aspects than the traditional physics-based modeling in computational chemistry. It is in fact much more about data. For example, to be able to retrieve and understand data from free websites such as ChemSpider, PubChem, or EMBL, or proprietary information from intra-clouds. Or, to recover all known structures of kinases (see picture on the left).  Another application, in an experimental setting, is to steer a high-throughput screen that determines by robotics the aggregation propensity of a hundred thousand different chemicals. Another, very challenging, example is in the automatic reading of intellectual property reports. For all these novel aspects, our scripted workflow and python interface offers exciting possibilities, for instance by digital downloads, followed by physics-based or data-driven computations.  Such advanced modeling is of course for graduate and postdoc level.

RESULTS

CULGI software has been used in undergraduate and graduate teaching and graduate research.  For professors that have bought a research license to CULGI, license for teaching are free, including free licenses for home PC’s of students.

Download a COURSE

We have been using CULGI in undergraduate teaching for more than ten years. We have an extensive suite of theoretical introductory readers, workflows, exam questions, and take-home exercises that we can share with you. The course is suitable for undergraduate and graduate teaching. If you are interested,  to receive a copy, please send us an email.

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