Starter guide - BNNLab/BN_Group_Wiki GitHub Wiki

1. Getting started

Supervisor Contact

Prof. Bao Nguyen 
Room G17, School of Chemistry 
Tel: (011334) 30109 
Mobile: 07833924420 
Email: [email protected] 

Once you have the university's username, you should inform Prof. Nguyen so you can be added to the group Teams. This will give you access to group-wide messages and help from other group members before you arrive in person. The best way to reach Prof. Nguyen in non-urgent cases is by email and messaging via Microsoft Teams.

Accommodation

Most students and postdocs rent properties from outside the university, but for students and short term placements, the university provide an accommodation service, which can be found at http://accommodation.leeds.ac.uk/.

2. Research standards

Coding

The code generated during your research should be regularly backed up into a designated GitHub repository. This is also part of the PhD thesis submission. You should register for an account on GitHub and let Prof. Nguyen known so you can be added to the correct repository.

The main programming language in the group is Python and bash scripts, although other languages may be used when required.

ChatGPT, Co-pilot and similar services

These are great tool with one draw-back. Other than Co-pilot through Leeds' registered logins, the ownership of the data in your queries is a grey area legally. We prefer to run local LLMs to support our work on our own computers. That way, potential intellectual properties are not compromised. Instructions on how to do this can be found at Running local LLMs.

Characterisation data

All novel compounds (cannot be found in Reaxys) will have to be fully characterised (1H, 13C NMR, IR, UV (if UV active) and MS, and others if required). If your compound is known, then you will need to match 2 of the above data with literature values. If the literature does not provide the full characterisation of the compound, it is your duty to the community to do it. All these need to be included in your report.

A form for this has been conveniently prepared in the group folder on Teams.

NMR and store registration

Separated forms can be collected from store for these registration.

All NMR users need to be trained by Mark Howard (NMR room) before using the service. After that you will need to contact IT to generate your NMR username and password. Instructions for downloading NMR data can be found at NMR data.

Housekeeping

Please make your best effort to return chemicals and equipments back to their original place right after use. Failing this will affect other colleagues in the lab. All researchers in the lab are expected to keep their working area tidy and organised, particularly outside their fumehoods. Music and radio are allowed, but the volume should not be too loud to interfere with the safety of the lab and other groups. Headphones are prohibited in the lab for obvious reason.

New chemicals should be labelled with the group name (BNN) and the date of arrival to keep track of their quality. They also need to be entered to the group chemical database before use.. It is important to update the database when a chemical is spent or its location is changed.

Group data and computer related issues

See [Data storage], IT and software.

3. Lab practice

Working hours

The normal working hours are 8.30 – 18.00, week days only. However, reaction time does not always conform to this. Work outside these hours is allowed for PDRAs and PhD students provided that there are other workers within line of sight and ear shot. NO ONE is allowed to work alone in the laboratory, at any time! This is the most important safety rule you need to know. Generally, as undergraduate students you must not work without someone more senior in the lab. Graduate students and PDRAs can work outside these hours, but must sign-in the after-hours log book.

Lab safety

A safety induction will be given at the start of your placement, outlining the emergency procedures and contacts. No eating and drinking is allowed in the lab at any time. Your bag should be left in the write-up area. Lab coats and gloves must never enter the write-up area.. If you are the last person who leave the lab, then it is your duty to make sure everything is safe, including what is in other people’s fumehoods.

For overnight reactions, you'll need a form signed by Prof. Nguyen or a PDRA which you will display clearly next to your reaction.

Please remember that all experiments need to have their COSSH form properly filled in and countersigned by Dr Bao Nguyen or a PDRA. Any change in scale or procedure to an old experiment would result in a new COSSH form to be signed. Reactions on scale >5g generally need a new COSSH form each time.

All new members are strongly advised to go through the School's safety rules and safety procedures before starting lab work.

Lab-book

All experiments need to be included in your lab-book, WITH PROPER RISK ASSESSMENTS (the risk associated with every chemicals you use need to be evaluated) and signed by Dr Nguyen or a senior PhD student/postdoc before starting. If the experiment is a repeat, then you won’t need new signature, but will still need to carry out the risk assessment in the book. A repeat here means the exact same reaction/experiment, with no increase in scale. Scaling up is always very dangerous!

The lab-book must stay in the lab, especially if you have a reaction overnight. Please feel free to make a copy of it if you are writing up using the photocopier machine or your mobile phone.

4. Internal services

Store orders, waste disposal, other admin forms, access to MS, NMR, etc. can all be found at the group Sharepoint.

5. Data

Storing and managing research data is an essential part of a researcher's training. New members should consult the page on Data storage before they start.

6. Other resources

7. Useful and free software

These changes all the time as technology improves. The current potentially very useful software are:

  • Topspin (https://www.bruker.com/en/products-and-solutions/mr/nmr-software/topspin.html) from Bruker: Best software for NMR processing, with very advanced features for power users. Now free for academic use and can be installed on Windows, MacOS, and Linux.

  • LM Studio (https://lmstudio.ai/): The software you need to run a local LLM model on your desktop computer. The other option is Msty.

  • Zim wiki (https://zim-wiki.org/): Free, open-source and portable wiki which can be put inside a folder in your OneDrive account, giving you access to all your notes (including images) from anywhere, any platform. Zim wiki is also very simple to understand and manage.

  • Sublime Text (https://www.sublimetext.com/) is available cross-platform, fast and can be customised for coding. Once set up, it can manage conda environments, has full Anaconda IDE capabilities and run Python script directly.

  • Visual Studio Code: Slower than Sublime Text, but with more bells and whistles, if you like that sort of things.

  • OneNote is an extremely useful cross-platform note-taking software. It's greatest advantage is that it sync with your university account, and the notes are sync across all devices, including your mobile phone.

  • Freefilesync (https://freefilesync.org/download.php) is a very useful and free synchronisation tool to back up your data. An encripted 32 or 64 GB usb stick is recommended for this (in addition to your OneDrive).

  • Insync (https://www.insynchq.com/) is a cheap tool to sync with your OneDrive in Linux, allowing seamless transition between the computer at work (Windows desktop) and your own Linux computer.

  • mechaSVG (https://github.com/ricalmang/mechaSVG) is a very useful tool to produce nice pictures of computed reaction pathway.

  • Overleaf.com: This web tool is for writing Latex documents (theses, reports, and manuscripts), including collaborative writing. It works across all operating systems and is very convenient when moving between different computers. The draw-back is the need for internet access. University of Leeds as a pro license for all students and staff members.

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