Resources

Contents

Information technologies that may be useful for course work and research

Scientific literature

• This Western Libraries’ Tutorials is a very nice series of videos for accessing different types of information.

• If you are trying to access journal articles from home (not within the UWO domain), this Western Library URL generator is probably what you need.

It is difficult to keep up to date with new publications in your area(s) of interest. In addition to standard Google searches, I use some of the following strategy each day.

• NCBI’s PubMed Provides access to almost all scientific publications. ¹ The NCBI has a tool where you can receive daily updates (by email) of all abstracts containing specific keywords.²

• bioRxiv preprints and now medRxiv preprints It is becoming increasingly common to submit manuscripts before publication to the preprint servers such as \({\tt bioRxiv}\). In fact, my group finds that there is quite often a year’s delay between when a preliminary (unrefereed) version of a manuscript appears as a preprint and when it appears in a journal in its final version.³

• Twitter specifically #academictwitter In addition to a platform that allows questionable right wing politicians to tweet questionable policy decisions, Twitter cannot be ignored as a valuable tool for following your scientific community. ⁴ I highly recommend that each student open a Twitter account for their “professional” purposes and follow members of your community. This includes journals and preprint servers who regularly tweet new papers.⁵

• Google Scholar Not surprisingly, this is a very powerful search engine for academic groups and publications. I recommend every student to establish a profile at Google Scholar.

• Otherwise, I greatly rely on my group to post interesting articles to our \({\tt Slack}\) workspace and to give mini-presentations of potentially interesting papers in our lab meetings.

• Cancer Visualizations has some beautiful images of cancer-related processes and detailed signalling maps.

Bioinformatic resources

• National Center for Biotechnology Information (NCBI) A huge resource from the USA that houses a vast spectrum of biological data and datasets, and bioinformatic tools.

• European Molecular Biology Labs (EMBL) and EMBL-European Bioinformatics Institute (EBI) are the European analogs to the NCBI with similar mandates and scope.

• The Cancer Genome Atlast (TCGA) program. TCGA, which is USA based, contains high-throughput profiles for several large patient cohorts across different cancer types. The availability of multi-modal high-throughput profiles conducting in a uniform manner across these cohorts opens up many analysis opportunities.

• International Cancer Genome Consortium (ICGC) is similar to TCGA but an international consortium across more types of cancers.

• Google Drive An excellent and convenient collection of tools (documents, images, spreadsheets, presentations) with lots of storage space. This is cloud-based so teams can work on documents simultaneously.

• Zotero or Paperpile It is really important to develop your library of bibliographic references, but it can certainly be challenging to keep all the references organized. Also, it is time consming to manually enter all the details of reference. There are many good tools out there; we tend to use Zotero as it is well integrated with Google Docs (for text files).

• Slack We will use this non-stop in the course. There are alternatives including open source efforts but for various reasons we choose \({\tt Slack}\) for all of our laboratory-related work. Any of these tools are far far superior than email (yikes).

Time management

There are many software packages for designing, executing and managing large projects that involve many people. Most of these packages are built for companies. However several are particularly useful for modern life science labs.

• Trello This is a project planning tool that is quite handy. It is not life science specific and could be used for almost any time of proect or event that is complicated to plan. Some members of my lab use it.

• Labscrum This is a strategy for conducting academic scientific research. It is a way of organizing a group, and provides a method to assist in tracking progress of projects and researchers.

• Toggl This is an app that allows you to manage your time. Basically, you can keep track of how long you spend on different tasks during the day. Many private consultants use this type of tool to record how long they spend on a client’s project for billing purposes. It is also useful if you have trouble managing your study and research time.

Resource management

Especially with wet labs, a consistent effort is needed to order, track and invoice reagents, kits, and other expendables. Moreover, there is a need to precisely and accurately handle samples. For instance, as we process samples donated by cancer patients, we have a moral obligation to ensure that the material is not lost or mislabeled. Our lab certainly finds it challenging to maintain a “chain of custody”. We have experience with several software systems.

• Quartzy and Benchling are both nice software systems, each with their pros and cons.

• Snipe-It We recently installed this system as a way to generate QR- (or classic bar-) codes. Basically, you can print out QR code stickers and associate each QR code with one item (reagent, buffer, sample, computer, eraser) in your lab. You need only a cell phone with a camera. You can purchase cheap special sticker paper that survives autoclaves and -80 freezers.

Markdown

The slides and website for this course were developed in Markdown, specifically a dialect deigned for R (\({\tt RMarkdown}\)). Fluency in Markdown is a useful skill to have as more and more tools and information migrates to the cloud.

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• The Plain Person’s Guide to Plain Text Social Science: A comprehensive explanation and tutorial about why you should write data-based reports in Markdown.
• Markdown tutorial: An interactive tutorial to practice using Markdown.
• Markdown cheatsheet: Useful one-page reminder of Markdown syntax.

Modern lab notebooks

• These are interesting short articles on different approaches towards keeping lab notebooks, and the pros and cons of electronic laboratory notebooks (ELNs) versus traditional paper notebooks. E Pain (2019) Science and R Kwok (2018) Nature.

• I used a tool called Goodnotes. Others in my lab use Evernote.

• I now use Notion. This is software that really integrates many tools into one coherent framework. If everyone in a group is using the software, it is very easy to share notes, images, calendars, and other common information. As it is cloud based, the information is available anywhere to all members of the group.

Citations and bibliography

⁶ You can download a BibTeX file of all the non-web-based readings in the course.