This page contains the websites, guides, and managers we have found essential to a functional PhD, both at the bench and on your laptop or the web. These tools will help you address questions including:
- What combination of restriction enzymes and buffer should I use?
- How do I calculate that molarity again? I’m doubting my math!
- How can I visualise this DNA sequence?
- Where can I get a brain anatomy map?
- What tool should I use for citations?
- I have too many tabs open with papers I should read! Where can I save these and come back to them?
NEB Bio Calculator–Converts mass to moles, calculates molarity and dilutions, designs sgRNAs, identifies enzymes and double digests, estimates melting temperatures for primers, etc. Tools for molecular biology.
SnapGene: for planning DNA manipulations and for visualizing sequences; especially helpful for plasmids. The free version, SnapGene Viewer, allows you to view sequences and identifiable elements within them (ORFs, restriction enzyme sites, primer binding sites, etc), while the full version available for purchase, SnapGene, allows you to virtually manipulate the sequence with restriction enzyme digests, ligations, insertions, and deletions.
NEB Restriction Enzyme finder–Use this tool to select restriction enzymes by name, sequence, overhang or type.
NEB Double Digest Finder–Use this tool to guide your reaction buffer selection when setting up double digests, a common timesaving procedure.
1Degree Bio –Find reagents and reviews separate to the ones on the product website.
Mouse Book: Provides citable, catalogued information about mutant mouse lines browsable by phenotype, SNPs and indels, genes, and rare human disorders. Mousebook also provides avenues to order mouse lines.
Tocris Molarity Calculator : Finding molarity a pain? This calculator can save you time and hassle.
Laboratory Skills: Want an overview of some basic techniques and skills, this site may be able to help.
GENSAT project: This site can show you just about any mouse brain anatomy that you could possibly need.
Writing and Organization
When writing, be it academic or more general, few things are as frustrating as referencing. Except maybe forgetting where you read something! This page is designed to highlight tools that can make life easier with writing in any context.
Benchling : A life sciences data management and collaboration platform. This is essentially an online lab notebook that allows you to organize experiments, map them on a calendar, and link notebook entries to different protocols.
There are a variety of different reference or citation managers that help make your life easier. Which one you pick generally comes down to doing a bit of research and finding your personal preference.
These programs generally allow you to save a reference of something from the web, upload documents from your computer, access your library wherever you are and add references straight into word documents. No more doing referencing by hand!
Mendeley and Endnote are two of the most popular referencing websites, with both having a wealth of “how-to use” guides (official and un-official). Some universities also run courses on how to use them.
Backing up your work
After you have spent all that time, sweat and effort on your writing the most devastating thing that can happen is it gets lost. Most people will now have several places they prefer to back their work up, but if you want even more security, or the option to access your work on the go there are several useful options.
Evernote – There are both free and paid versions. It allows you to upload and edit files online, from a desktop app and from mobile apps. It is very useful but the user interface can be a bit of a pain, and editing on documents created on the program can be frustrating.
Dropbox– Once you add your files to Dropbox, you can access them from any device, anywhere. You can also share securely with others, leave comments, and create online documents.
Google Drive– You can upload files from your computer or create documents, spreadsheets, and presentations online. You can share with others and track comments.
Hard drives–Some people use actual physical devices to save their work rather than relying on the cloud.
Before worrying about where to store your work you actually need to have something written. The following resources are helpful for ensuring your writing is as good as it can be, and it appropriate for what you are writing about, ie science!
Wellcome Trust – A series of collected advice for various aspects of scientific writing, from starting a science blog to interviewing someone.
New Scientist: Science Writing– You’re a human, so write like one! These tips are for public engagement/science communication writing.
New Scientist: Academic Writing–Tips for improving your academic writing. This article also provides links to other academic writing resources.
Bad Science – A picture guide to spotting bad science.
Research Gate: Ask other scientists questions about your work, the scientific community is a great source of information and can be specific to your needs.
Finding scientific articles in general, but especially those that are actually relevant can be very time consuming. So we have compiled a list of tips, tricks and sites that help speed the process along.
Google Scholar – the simplest search engine you can use. At its most basic you just enter your search terms the way you would for normal google. If you are affiliated with a university you also have the option under settings to show paper access links for your university.
How to Get the Best From Google Scholar Top 5 Tips – A short video tutorial on using Google Scholar from Cardiff University.
Web of Science – A search engine providing access to scientific resources subscribed to by your institution.
Scopus – A search engine for scientific articles which requires institutional login.
Pubmed – A popular search engine for scientific papers and abstracts, often with a medical focus.
NCBI – This is a U.S. government-funded national resource for molecular biology information. It hosts PubMed and Genome Browser.
Sparrho – This a useful and free website that will search various sources based on your criteria to provide you with articles, patents, grants and much more. You can have a number of different channels with different key search terms, set up email alerts for new content, and create pin boards to keep track of papers you want to look at again.
One way to reduce the time spent searching for papers, and to stop you having to use the same search terms over and over again, is to set up email alerts for new papers on your topic. This video from NCBI shows how to do this on their system.
Zetoc is another version which searches particular journals and articles for your key words and then alerts you to regular papers regularly.
Once you have published in a journal you can also set up alerts emailing you every time your article is cited by someone else, allowing you to follow its impact. This link gives you a list of ways you can set this up.