BioScope

A UC Davis Graduate Student Blog

Category: scientist_2.0_toolsforsuccess Page 1 of 2

The Molecular Biologist’s (Virtual) Toolbox

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On August 11, 2020

In scientist_2.0, scientist_2.0_toolsforsuccess

There are many useful tools out there to assist you with plasmid mapping, primer design, and DNA sequence analysis, so many that it can be difficult to keep track of them all. Thankfully, Addgene has made it simple to find the exact tools you need with their Early Career Research Toolbox, which lists most, if not all, of the most useful free research tools available online for molecular biologists. In it, you’ll find tools to help you view, edit, and create plasmids, manipulate DNA sequences, identify and compare DNA and protein sequences to free online databases, facilitate cloning ligation reaction calculations, and more.

Even if you’re certain you already have all the tools you’ll ever use, I advise you to give Addgene’s toolbox a peek. You may just find a new application you didn’t know you needed.

May your thirst for knowledge never be quenched,

Nina Cueva

 

Resource suggestion made by: Yulong Liu

Edited by: Yulong Liu and Sydney Wyatt

Organize Space and Time to Keep Sane in Isolation (Or Otherwise)

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On June 1, 2020

In scientist_2.0_toolsforsuccess

Like most (if not all) of us here at Bioscope, you may be struggling with how to remain productive while doing primarily everything in isolation. You may have even found yourself attending classes, working from home, and watching Netflix, all from the same, sunken, spot on your bed more times than you’re pleased to admit. Although this may have worked for the first few months of quarantine, by now you’ve probably noticed how unsustainable this habit really is. 

In the Youtube video “Lockdown Productivity: Spaceship You,” CGP Grey illustrates how living in such a disorganized, unstructured manner undermines our ability to maintain our individual “spaceships” by impairing our mental and physical well-being necessary for its operation. Learn the simple, though effective ways of keeping your sanity and maximizing your productivity when operating in a finite area by making the most of your space and blocking out areas to work, sleep, exercise, and couch (apparently couch is now a verb).

I truly believe these techniques are helpful no matter how small your functional area and regardless of our current coronavirus pandemic. I hope you think so too.

 

May your thirst for knowledge never be quenched, friends,

Nina

 

Resource suggestion made by: Yulong Liu

Edited by: Yulong Liu and Keith Fraga

Resources to Expand and Strengthen Your Skill Set

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On April 28, 2020

In scientist_2.0, scientist_2.0_toolsforsuccess

Would you like to supplement what you’ve learned in a previous course or a legitimate way to expand your expertise? Check out these nifty online resources sure to assist you in your academic and professional endeavors.

 

Coursera is an online learning platform brimming with educational opportunities. Browse through thousands of free online courses from a plethora of disciplines taught by reputable professors from distinguished universities and companies. Through Coursera, you can even obtain certificates and degrees proven to increase salaries and marketability, although these features require payment. Fear not, as payment for these features is very affordable. If money is still an issue, you can try applying for financial aid and scholarships offered through the platform itself.

 

If you’ve taken a computer programming or data science class but were left unsatisfied with your handle on the subject, consider signing up for a workshop organized by The Carpentries project. The Carpentries is a non-profit, community initiative based in California that strives to provide dependable and consistent fundamental computational and data science skills globally using evidence-based teaching practices.

 

If you can’t afford to pay for a Carpentries workshop, that’s okay; the UC Davis students, faculty, and staff of the College of Biological Sciences have you covered. They’ve graciously compiled these Interdisciplinary Tutorial Resources for those in need of some additional guidance in the areas of R/Rstudio, Python, Statistics, Machine Learning/AI, Genomics, and Light and Electron Microscopy.

 

May your thirst for knowledge never be quenched,

 

Nina

 

Resource suggestions made by: Yulong Liu, Ellen Osborn, and Sydney Wyatt

 

Edited by: Yulong Liu and Sydney Wyatt

Which Colors Should I Use? The Importance of Color Combinations in Scientific Figures

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On February 26, 2020

In scientist_2.0, scientist_2.0_toolsforsuccess

When creating scientific figures to best showcase your data, it is easy to overlook the importance of color scheme. When choosing color combinations, we tend to make our decisions predominately by what looks most appealing to our own eyes. However, it is crucial to remember that not everyone perceives color the same way. In the past, scientists often created fluorescent images and heatmaps using a green/red color scheme, making figures practically indiscernible by those with varying forms of colorblindness. The following article can help you learn to create illustrations that provide just as much contrast with arguably more visual appeal than a  green/red color arrangement, increasing the accessibility of your research. 

-Nina

 

Article on color-blindness and scientific figures. 

https://www.ascb.org/science-news/how-to-make-scientific-figures-accessible-to-readers-with-color-blindness/

 

A nifty web tool for helping you choose colorblind-friendly color schemes. Make sure to click on “colorblind safe” and “printer friendly” checkboxes. 

http://colorbrewer2.org/#type=diverging&scheme=PRGn&n=3

 

 

 

 

Edited by Keith Fraga

Source suggested by Yulong Liu

 

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

Making scientific figures with Adobe Illustrator

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On November 6, 2019

In scientist_2.0, scientist_2.0_toolsforsuccess

Illustrations are often an integral part of a scientific manuscript, especially when conveying complex ideas and data. Additionally, a beautiful illustration is just so nice to look at. Lucky for us, we don’t have to spend years to master drawing those illustrations anymore like in the good ol’ days because there are many software options available to help us make these illustrations. Adobe Illustrator is one of the most powerful tools out there for creating illustrations and is more versatile than the more commonly used Powerpoint. However, it is something that you might not be familiar with and with a slightly steeper learning curve. I came across a retweet from our very own Sydney Wyatt about this Adobe Illustrator guide wrote by Connie Jiang, an MD/PhD Student at UPenn, and I was amazed by how useful it was for a beginner user like me. The guide is orientated for scientists. It covers basic usage and also a range of specific topics such as design scale bar, making poster templates, and color-blind friendly colors. I hope you will find this guide useful, and make the transition from Powerpoint. 

–Yulong 

 

Blog post

http://rajlaboratory.blogspot.com/2019/08/i-adobe-illustrator-for-scientific.html

Guide 

https://docs.google.com/document/d/1TXmbltzBPcApCcuJ9HLOIQgWPqKylrFRWRudrN-5vBE/edit#

 

Edited by Sydney Wyatt 

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

Informational interviews, a must-do for your next career move.

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On August 26, 2019

In scientist_2.0, scientist_2.0_toolsforsuccess

I truly believe informational interviews are one of the most important things you need to do when you are planning your next career move. An informational interview is a process by which you can access all the insider information about your next job that you most likely not going to find online. Sadly, I found the majority of the graduate students that I have talked to do not really know what it is or the purpose that these interviews serve. For those who have never heard of informational interviews before, it is a non-formal conversation to seek information about specific careers and companies. Although it’s not something from which you can be hired directly, the valuable information that you can get from this can give you a significant competitive edge and some even have received an actual interview directly from their interaction with the interviewer. In my personal experience, I did a couple of informational interviews for industry postdoc positions, and I found there are major differences in the optimal ways to apply for those same positions between companies. Here is a great video from Cheeky Scientist with useful tips and mistakes to avoid when you are conducting an informational interview, and the video is specifically tailored to graduate students. 

-Yulong 

 

https://www.youtube.com/watch?v=ZifvsYPpqH8

 

Edited by Jennifer Baily

This video was originally brought to my attention by the FUTURE program’s course. The FUTURE program is a career exploration/preparation course that I highly recommend to everyone. Here is their website if you are interested https://future.ucdavis.edu/  .   

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

Tweet your way to success in science communication

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On July 15, 2019

In scientist_2.0, scientist_2.0_toolsforsuccess

Do you have a Twitter? Do you use Twitter to communicate and promote your science? In the past couple of years, Twitter has developed into the preferred social media platform for scientists to communicate their science to a broader audience. You may have heard of this already and even noticed that your favorite conference now has an official hashtag. However, it can be daunting for many people to make the leap into the Twitter-verse. That includes me. This blog article was co-authored by a UCD graduate student and contributor for Forbes, Priya Shukla(@priyology), is a great beginner guide for scientists who want to start their own Twitter. It also contains many useful tips and suggestions tailored for scientists to get you up running in no time. As the article suggests, communicating your science to a broader audience can help you become more well known in your field and even may help you to find your next job. 

https://www.thexylom.com/scientists-meet-twitter

-Yulong Liu 

 

Edited by Keith Fraga

This article was originally introduced to me from the FUTURE program’s course. The FUTURE program is a career exploration/preparation course that I highly recommend everyone to take. Here is their website if you are interested https://future.ucdavis.edu/  .   

 

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

Keep calm and read on – Top tips for staying on top of your reading

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On June 13, 2019

In scientist_2.0, scientist_2.0_toolsforsuccess

Do you know there are about 2.5 million papers published each year? It certainly can be difficult and daunting to keep track of the relevant papers that are related to your research. You may already know about using Google Scholar or PubCrawler to keep you updated, but are you using them efficiently? I have seen many people’s weekly update with hundreds of papers because they are using very general terms. It’s understandable that you don’t want to miss anything, but you are going to spend so much time combing through them. Here are the “Ten tips to stay on top of your reading during grad school” from the publisher PLOS, including tips on how to optimize your search terms by using Boolean operators like AND and OR.

https://blogs.plos.org/thestudentblog/2017/01/12/ten-tips-to-stay-on-top-of-your-reading-during-grad-school/

 

-Yulong Liu

 

Edited by Emily Cartwright

Suggested by Keith Fraga

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

Mastering the art and science of good presentation design

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On December 5, 2018

In scientist_2.0_toolsforsuccess

Powerpoint presentation is one of the most effective ways to communicate our science. However, mastering the art of presentation can be a long and enduring journey. There are two parts of a good presentation. One is about speaking, and the other is the actual presentation itself. If you have a fear of public speaking, please check out our previous post on “combat the public speaking fear”.

This post focuses on the design components of a good presentation. Luckily for us, there are many fundamental principles that you can learn from this short-ish video to help you achieve that mastery. This video, suggested by Hongyang Hao from Dan Starr’s lab, features Stanford neurologist Susan McConnell. Susan McConnell is a world-respected scholar and science communicator with iBiology. She is a member of both National Academy of Sciences and the American Academy of Arts and Sciences, and she is also both an HHMI scholar and a Pew Scholar. The list goes on and on.

You may know some of the recommendations already from the video, especially, if you are a UC Davis BMCDB graduate student who went through our awesome rotation class. However, I’m sure there is much more new information that you can learn from this video. Also, it is just a good practice to systematically evaluate your presentation skills once a while, and make sure your presentations don’t have the pitfalls mentioned in the video.

Mentioning the rotation class made me remember my first presentation in that class. All I can say is “ughhhhh”. I’m so glad it is better now.  

Yulong

Want to see more awesome videos like this one? Make sure to check out iBiology and their videos on the importance of giving a good presentation and more tips on creating effective slides.

 

Suggested by Hongyan Hao

Edited by Anna Feitzinger, Keith Fraga

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

Ain’t nobody got time for bad graphs

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On October 16, 2018

In scientist_2.0_toolsforsuccess

The above graphs were made from data of an anonymous 4th-year graduate student’s drinking habit, as he became an alcoholic in denial. Although the graphs were made from the exact same data, it’s obvious they give different perceptions of what the data is representing. One of the graphs indicates an alcoholic graduate student slowly increasing its alcohol consumption. The other graph suggests a more destructive trend: sobriety to a full-blown alcoholic. Bad data representation can be just as detrimental as bad data. Anna Feitzinger from the Lott Lab sent me this very useful website discussing common problems faced when graphing data. It has example problems, clear solutions, and some even have convenient practice R code.

https://www.data-to-viz.com/caveats.html

 

Yulong  

 

Suggested by Anna Feitzinger

Edited by Sydney Wyatt

For any content suggestions or general recommendations, please email to UCDBioScope@gmail.com and put science 2.0 in the title.

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