Accessing instrument data
Data recorded on most instruments within the teaching laboratories is automatically made available for electronic access. Data is copied onto the teaching labs data server shortly after acquisition, typically within 15 minutes of data collection being completed.
Teaching Labs Webfiles server
Teaching Labs SFTP server
sftp://sftp.york.ac.uk/shared/storage/chemtl
Instrument types
Instrumentation in the Teaching Laboratories is broadly grouped into two methods of use. There are instruments which you are able to walk up to, use, and immdiately obtain your results, for example IR, and UV-Vis. There are other instrumentation which relies on data submission, where you prepare a sample for this to be added to an instrument queue which will then be recorded later (usually overnight). The approach to finding data varies depending on the method of submission, with details for each given below.
Walk-up instrumentation
Instruments which you are able to walk up and run your sample immediately are generally simpler to locate your files. When recording data it is important that you make a note of the filename which is created the time of data collection. The filenames usually consist of three parts:
You will need to know the name of the PC used to record the data. These are usually displayed on a label on the PC monitor. PCs in teaching labs start with 'CTL' (standing for Chemistry Teaching Labs), then the next bit of the name usually relates to the technique being used (eg IR) and an instrument number. For instance a PC used for recording IR might be named 'CTLIRPC1'.
The next part of the name consists of the date. This is given in the format yyyymmdd (year, month, day).
The final part is the time the measurement was taken, and is in the format hhmmss (hour, minute, second). Note that some instruments record the time at the start of the measurement, and some the time when data collection finished.
When recording data, you should make a note of the PC name, along with the date and time you recorded the sample. This filename will also usually be displayed by the instrument in its software, so that you can record this into your lab book, or if not, record the time from the clock on the PC, and the PC name which will be on a sticker on the monitor.
A typical filename might be "ctlirpc1_20200313_155702", which would correspond to a teaching labs (CTL) PC connected to IR number 1 (IRPC1), recorded on 13/03/2020 at 15:57:02.
Sample submission instrumentation
For other instruments, samples may need to be submitted to a queue, and samples will be automatically loaded by the instrument using an autosampler. For example NMR, HPLC and GC may use autosamplers. For these samples, you will typically complete a submissions form and label your sample with a submission number. These submissions can be accessed from the relevant and your sample filename can be found by looking in the submission spreadsheets. You may find columns in the spreadsheets which allocate your sample to a particular instrument (eg GC1, GC2 etc) and to a particular autosampler position or experiment number. These spreadsheets will allow you to identify the data you need to access.
Finding the right location to look for data
Data is stored inside subdirectories which are organised by instrument type. Details for where to locate data for a particular instrument can be found in the relevant instrument pages. Generally it is easiest to go to the instrumentation page for the data you want to access, and copy the link provided on that page.
Accessing data
There are two methods provided to access data collected in Teaching Labs. Both routes give access to the same data, but differ in their use. Webfiles is very simple to use and is good for locating and downloading individual files, whereas the SFTP service is better for downloading larger quantities of data (including folders), but is a bit more complicated to use.
Both services are provided and managed by IT Services, who also provide their own guides to their use (for multiple operating systems) which are linked below.
Webfiles
The Webfiles service will work in any web browser and allows files to be downloaded one by one from the data directories. This service requires no additional software, and works in all web browsers. The link below will take you to the service, where you can then locate your data from the instrumentation folders (see notes below on identifying data folders).
If you are accessing from Teaching Labs, the pages will display without needing to log in. If you are accessing from anywhere else (on or off campus) you will need to log into the server using your university username and password.
SFTP
The SFTP service (Secure File Transfer Protocol) provides a more functional interface which allows the downloading of multiple files at once, or entire folders of data. The IT Services provided guides contain step by step instructions to connect to the service, which will need to be accessed using your university username and password (and two-factor authentication) whether you are on or off campus.
The SFTP service is located at:
Once you have connected to the service, you will need to browse to:
/shared/storage/chemtl
You can then browse into the individual instrument folders from which file(s) or folders of data can then be downloaded to your computer for analysis.
Identifying the data folder
In order to access your data, you will first need to identify the folder location for the data on the Teaching Labs Data Server. Visit the appropriate Instrument Webpage for the data you are trying to access and locate the folder name in the 'Accessing Data' section. The page will also provide information on the formats available for the instrument data, and the filenaming conventions used by that instrument.
Data formats
Data is collected in a wide variety of different formats, and the provide details on the formats provided for specific instruments. In general these can be categorised as:
Automatically produced PDF results, eg a spectrum or chromatogram, which has been automatically processed by the instrument software
Data for reprocessing, which can be downloaded and processed in another programme (e.g. Spectrus Processor). This allows specific analysis of data, zooming and picking of peaks etc.
Raw data in text/number format, e.g. kinetics results from a UV-Vis spectrometer. These are most commonly in CSV format.
Propriatory data which can only be read by the software on the instrument PC used to record the data.
In general, in year 1 you would expect to be using the PDF files which have been automatically produced. In year 2 onwards, you would usually be expected to be reprocessing your data.