# Very useful software that will make your life a lot easier

## 1. RStudio / R

If I had to decide which one software I would take to a remote island, it would be R (RStudio). The software environment R is much more than the statistics tool it started out as. It is a Swiss army knife of analysis tools and there is little that R cannot do for you. R itself is a command line tool with RStudio being a graphical user interface (there are a few GUIs for R, but I like RStudio the best).
R is open source and the packages that are available (think of it as add-ons or plugins) cover pretty much any analysis or visualization that you can think of and are developed by a worldwide community. Plus, it is quite easy to make workflow and even custom scripts in R, once you get the hang of it. Get R [here](https://www.r-project.org/) and R Studio (which needs prior installation of R) [here](https://rstudio.com/products/rstudio/download/). There are very many good tutorials for R, e.g. [here](https://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf), [here](https://www.datacamp.com/courses/free-introduction-to-r) and [here](https://www.guru99.com/r-tutorial.html). And also for RStudio, e.g. [here](https://data-flair.training/blogs/rstudio-tutorial/). Together wirh Isabella Hrabe de Angelis I have made an R-based workflow for microbial communiy analysis named [VisuaR](https://github.com/EmilRuff/VisuaR). If you have amplicon sequences (processed with dada2) VisuaR does most of the classic community analyses. We extensively commented the workflow to make it easy for beginners to follow.

## 2. FIJI (FIJI Is Just ImageJ)

FIJI (short for: FIJI is just ImageJ) is an image processing and analysis tool. Similar to R it is open source and supported by a worldwide community developing plugins for almost any image file and analysis method. From automated cell counting to 3D animation. The FIJI menu looks a bit dense at first, but is surprisingly intuitive considering the vast amounts of features (the standard version already has). Get FIJI [here](https://imagej.net/Fiji/Downloads).
FIJI is especially useful, because it can read even most image files that are proprietary. For example [czi files](https://www.zeiss.com/microscopy/us/products/microscope-software/zen/czi.html) that are created when using the [ZEN software](https://www.zeiss.com/microscopy/us/products/microscope-software/zen-lite.html) featured in Zeiss microscopes.

## 3. Inkscape

An essential part of research is the visualization of results to highlight key findings and make the results more accessible to an audience. Inkscape is a very powerful and open source vector graphics software that is very useful to make beautiful, scalable, high-resolution visualizations, figures, graphs, and flowcharts.

### Graphic design 101

In my opinion it is good (if not essential) for every scientist to have a basic understanding of aesthetics and graphic design. To make high quality figures for a paper or presentation it is good to understand the difference between the two color modes `RGB` and `CMYK`. The former is used for screens, the latter for print. More on color modes [here](https://en.99designs.de/blog/tips/correct-file-formats-rgb-and-cmyk/). There are also two fundamentally different image types, pixel graphics/images and vector graphics/images. Pixel graphics (also referred to as raster graphics, e.g. jpg, tif, png,) are usually small and easy to read and handle, but they cannot be scaled. The resolution of a pixel image is set and enlarging it will cause it to blur. Vector graphics (e.g. eps, svg, ai) on the other hand cannot be opened by common image software, yet they are scalable. In theory there is no upper limit on size, no matter how large the image is it will still be sharp. Find more info on pixel vs vector [here](https://en.99designs.de/blog/tips/vector-vs-raster-images/). Here is an interesting and brief posts about [PPI vs DPI](https://en.99designs.de/blog/tips/ppi-vs-dpi-whats-the-difference/).

## 4. Mendeley Desktop

Sooner or later (rather sooner) in your scientific career you will have to use a bibliography tool. Such tools are very useful when writing reports, theses, manuscripts and proposals. Everytime you want to cite another scientists work you have to include a reference to the respective publication. Doing this by hand is insanely inefficient and prone to errors. My favorite tool (after using others like EndNote and Zotero) is the Mendeley Desktop. It is a very powerful hybrid between a cloud-based database and a computer-based bibliography tool. It is supported by and active community, has many useful features and most importantly is open source. It can be downloaded [here](https://www.mendeley.com/download-desktop-new/).

### Citation Plugin

After installing and launching the Mendeley Desktop (no worries, it will not interfere or replace your computer desktop), install the Citation Plugin. To do that go to `Tools` --> `Install MS Word Plugin` I am assuming you are using MS Office, because it is still so widely distributed. There are Citiation Plugins for Keynote and LibreOffice as well, Mendeley will autodetect the right one. Find more info on the citation plugin [here](https://www.mendeley.com/guides/using-citation-editor). The citation plugin is the most important feature of the bibliography tool, as it allows you to insert references in your text and creates a bibliography at the end of the document. You can also choose or download the citation styles of specific journals and much more.

### WebImporter

Another handy feature is the WebImporter that can also be found and installed under `Tools`. It will give you a little icon in your Browser (Firefox, Chrome, etc) that enables you to download a citation (and pdf, depending on access options) with one click.

### Best practice tips

#### Keep the citation database clean

Often when references are imported something is wrong. This happens when `drag & drop` of PDFs, but also when using the `WebImporter` and other means. Most often the problems are resolved by clicking on the :mag_right: icon of the `DOI:` field. This causes Mendeley to `Lookup` the details. Sometimes `Lookup` fails, but in any case - even if `Lookup` is successful - quickly check if the information (titel, authors, pages, etc) is right. This has to be done once and never again, so it is worth your time. Your future self will be very thankful to not have to check hundreds of entries ever again.
P.S. If the DOI is not included you have to manually `copy` and `paste` it from the paper. It is essential information that you do not want to miss.

#### Include the PDFs

Mendely has a pdf editor that lets you highlight text or add notes. This is of course very useful for finding yoour favorite paragraphs and results. Also, you will find yourself in situations where you do not have access to journals that are not open access, or where internet access is lacking altogether. Having all pdfs that are relevant for your research available is priceless.

#### Respect your colleagues names

Whenever you add a new entry carefully check the author names. Many languages have glyphs that are considered special in English. Like the French `accents` (é,à,ô,...), the Czech `háček` (č), the German and Turkish `Umlaut` (ü,ä,ö) the Spanish `eñe` (ñ), the French and Turkish `cedille` (ç), and so on and so forth. The easiest way of getting to these glyphs is by longpressing the respective key, e.g. longpressing the `a` key gives you the 8 most common a-related special glyphs `ä,à,á,â,æ,ã,å,ā` to click on and choose. Admittedly in Mendeley it is not as easy as in Word, but respecting other languages makes it worthwhile. Special glyphs can also be made using keyboard shortcuts. There are many lists online, e.g. [here](https://https://slcr.wsu.edu/help-pages/keyboards-osx/).

## 5. Filezilla

There are many FTP clients. FileZilla is widely used and open source. It can be downloaded [here](https://filezilla-project.org/download.php?show_all=1). It is basically a window between your computer and a remote server. It shows you the directories on both machines and allows you to copy and transfer files and folders back and forth. Pretty much everything that an FTP client does can be done using the command line as well, however using commands is much more tedious.

Note: MacUsers have encountered a [bug](https://trac.filezilla-project.org/ticket/7175). After opening Filezilla the window cannot be moved, because the header is hidden. Press the `option` key and `left click hold` the lower border. Move the cursor up, the window should now scale smaller until it becomes fully visible.

### Connect

At the top there are 4 empty fields:
Host: enter the address of the server
Username: enter the username (of your account on that server)
Password: enter the password (of your account on that server)
Port: 22

The server connection will now be stored in the `Quickconnect` menu. Next time you will not have to enter all the details manually again.

### Make a bookmark

Make a bookmark to quickly access important folders.
E.g. `/Users/user/Documents/` on the local side (your computer) and `/users/users/Document/` on the remote side (the server).