Core biochemistry toolbox - software, databases, etc. to get familiar with

Transcript

exact tools and software that you're going to need for being a biochemist or a molecular biologist is going to depend on the type of research that you're doing but these are some core programs that everybody should familiarize themselves with because they're probably probably going to be using them so just a quick overview and then I have we'll post a link to a version with links so that you can then go and download these things and check them out so some first let's start with databases so the QR core ones if you're working with proteins even a product that's your first go-to place it's got the information about basically like every protein it has a lot of links to take you to other sites but here you can find um proteins from all different species you can compare these proteins learn about their sequences um their get links to their structures and that sort of thing and so those links to the structures are going to take you to the pdb so the protein Data Bank that has all the structures that have been solved from things like crystallography and cryoem if you want to then view those proteins you can use a structure viewer like um Chimera X or Primal these are really great for allowing you to interactively um work with these 3D protein models and then make really pretty figures if you want to figure out more about like the makeup of the protein there's this tool called a Spacey prop param that's really helpful for finding things like the extinction coefficient which is going to allow you to figure out the concentration of a pure protein based on its absorbance of UV light um it's also tell you things like the pi the isoelectric point which is really helpful if you're trying to purify the protein and want to know if it's like positively or negatively charged because you're trying to purify it with ion exchange chromatography which the kind that you use is going to depend on whether your protein is positively or negatively charged and so that's where you go to the pi and then the ph and that sort of thing okay so for nucleic acids your go-to sources um gen Bank this is like all the sequencing data really really awesome then it also has links to other sort other tools so this is through like the ncbi and they have things like rough um refseq and stuff which has the reference genome and this various difficult things and More in other posts but Jam bank is going to have like all the public um sequencing data blast this is really great if you're trying to search for a nucleic acid to see um you have some sequins and you want to see where it comes from or maybe you're trying to design primers and you want to make sure that those for your like your PCR you want to make sure those primers aren't going to bind places that you don't want um gem bank is really really great oh sorry blast is really really great for that you can also do things like um compare sequences to get like evolutionary information as well as they have things where you can go from compare protein sequences as well as protein to DNA and all these various various tools for things like that speaking of cloning and like PCR and stuff if you're wanting to work with plasma so like circular pieces of DNA you're going to need to design your cloning strategies you might be using like PCR you might be using restriction enzymes but you're going to need to know the sequence of those of those plasmids and be able to work with them and so you're going to want some sort of plasma viewer so a common one that's used is snap Gene there's snap Gene viewer which is a free version and then there's like a paid version so you can't do as much with the with this just the viewer but if you just need to view a plasmid it has a nice interactive um in your face I used CLC main workbench in my last lap that's one that you have to pay for but it has some nice features a totally free one is a a plasmid editor and they have some nice videos and stuff on YouTube as well there's also DNA star which has some free um version and benchling which also benchling is helpful for like e notebooks um so speaking of the notebooks that's um that you don't need any mode but well your lab might make you but so some labs they have everybody uses the same one so this might be benchling which is like Cloud features and things so that people can share notebooks and share protocols and that sort of thing you might just have your own personal notebook so I use endnote to keep a virtual notebook and I also keep handwritten notes so that I and I type up my handwritten notes into my virtual notebook and so I can cross reference things and I can search my notebook so I find that really helpful um okay so a couple of other things so in terms of staying organized you're going to also want to make sure that you organize your references so when you find papers you want to be able to then know where be able to locate those papers again and then when you're writing a paper or that sort of thing be able to cite them so be able to give those authors credit so you're going to want to use a reference manager something like mendeley zotero endnotes there's something now called like read Cube I think Pages there's various um there's various reference managers that you can use in order to keep track of your references and so every time you read a paper I recommend saving that reference into your reference manager even if you don't think you're gonna ever need that paper to cite it or anything you want to make sure that when you think back later oh did I I know I read that somewhere you can go and find the find the source for the paper okay um you also want to be able to find papers in the first place so the papers are coming out all the time and you need to be able to stay up to date the main places where you're going to find scientific papers so there's this thing called PubMed which is this database which has like all the information about all of the published papers and links to the to like the Publisher's website where you can download these papers there's also like Pub my Med Central which has all of the like openly accessible papers so that are free to read nothing behind the paywall so um there's also bio archive which this doesn't have published papers it says preprints so things that haven't gone through that peer review process yet but have been posted on bio archive and this is another common place where you're going to find papers and these are going to be really really hot off the press stuff in order to stay up to date with all these papers and preprints that are coming out you might want to just look into setting up RSS feeds and using an RSS viewer so bio archive all these different Publishers even PubMed you can set up alerts to and you can set up RSS feeds which are basically like these custom feeds when there's an article a new articles come out on a specific topic that you specify then that it'll go to like to this RSS feed and you can use an RSS viewer where you can then put these feeds together and so these are things like I use news blur there's also Feedly the old reader Inno reader Etc and this is going to help you stay up to date and you can also set like alerts on PubMed alerts on Google Scholar this sort of thing this is really really helpful for making sure that you're not missing papers as they come out so you can set like key key Search terms are key words that if or key authors and then if those people publish something if those terms come up then you'll get an alert um super duper helpful okay just a couple last things you're going to probably want some sort of vector graphics program and to get used to using that vector graphics program so this could be like Adobe Illustrator a free version is inkscape these are things that are going to allow you to make graphics and figures not just for fun stuff um but also for like serious stuff like making figures for papers or for presentations the really nice thing about a vector graphics program is it's working in like points and things it's basically telling the computer how to draw the figure rather than being an image and so you're not going to get it you can save it in ways and blow things up that they're not going to get all blurry and so if you're giving a presentation you want to have your figures in this high quality form so maybe something like a PDF where you can blow it up and it's not going to get all pixely as long as there's not actual pictures in there which would still get pixely but the words and the lines and all of these things will stay nice and sharp okay um also another helpful thing is to learn a bit of coding and so you probably comment most commonly probably you're going to be wanting to Learn Python so I have a couple posts on why it's important to learn python as well as some basic tips for using python um I like to use Jupiter lab and Jupiter notebook which are basically these Interactive coding tools that you can use on your computer and you can share files with other people you can basically these are interactive notebooks so you can be looking at the code well while you're making it you can then like run little Snippets of code at a time and it also has a nice interface that allows you to see what see easily see different features and that sort of thing so much more on it in other posts but I recommend that um so there's Jupiter lab and there's Jupiter notebooks interpreter notebook or like the python files that have these like that these interactive python files but then Jupiter lab can also work with other types of programming languages as well as um like just core bash and stuff so terminal type stuff um basically it can do more than just the Jupiter notebooks But it includes the Jupiter notebooks and also you might want to learn a little r if you're working with r I recommend R Studio which is a desktop application that you can use in order to interactively work with r which is another protein programming language it's used commonly in things like ecology various things like that and so much more on those in other posts but those are the key tools that you will probably want if you are a biochemist or it's been to be a biochemist or that sort of thing and then you're going to need to pick up more tools and based on what your project is and I will also link to a post I have with more more and more databases and tools for some of them are like much more specialized but I hope this helps give you an overview of the type of things that you should be getting familiar with if you are starting out on the Journey of becoming a biochemist and so I wish you all the best on the journey because it's really really exciting um and so hopefully this isn't go overwhelming it's meant to be helpful um and so hope it helps