This document is currently a very mixed bag. Many of these topics are discussed elsewhere on this site and I'll try to reorganize them, but that's likely to take a few months.
Site-licensed means that people who are part of a particular organization may use the resource with no additional cost. (Other forms of license include individual licenses and group licenses. The difference between a group license, which is also granted to an organization, and a site license is that the number of users of a group license is limited. This is the form of license for some software loaded on the departmental lab computers.)
The University of Tsukuba library has licenses for a few individual journals. I don't think I've ever accessed one that way. Most of its online subscriptions and archival access come via large bundling services like JStor and Science Direct.
You don't need to worry about this. In order to access these resources, you need to be logged in to TULIPS anyway. So just log into TULIPS (sometimes you have to be using a University network address, but I don't think the VPN works), search using TULIPS to find the resources you need, and if you're allowed to download them, you can just do it.
The Media Center (筑波大学 情報環境機構 学術情報メディアセンター) has site licenses for a variety of software which you can download for your personal computers and handheld devices. These include antivirus software, Microsoft Office for personal use, and Mathematica for personal use, as well as some statistical packages like SPSS whose terms I'm not familiar with. There is also a discount program from Apple. These are linked from the sidebar of the "Service" page for the Center:
https://www.cc.tsukuba.ac.jp/wp/service/ (Japanese)
Be careful about the English pages of the University. They are frequently incomplete, and sometimes out of date, compared to the Japanese pages. If you have a strong preference for reading English over Japanese, by all means try the English pages first. If you succeed, great! But if you don't find what you're looking for, don't give up: it may be on the Japanese page.
The Faculty of Policy and Planning Sciences has a databank project, which keeps locally-generated databases. It also has subscriptions to certain proprietary databases, such as Nikkei's. Most of these are linked or described on infoshako.sk.tsukuba.ac.jp.
(There are also scholarships from the International Student Center that foreign students should investigate.)
There are budgets at this University to support your research. I'm not aware of national or University-level budgets directly available to students (other than the Monkasho fellowships and PhD research grants). At the kenkyuka and senkou levels, there are budgets for travel to conferences that you can apply for, with my permission and recommendation. Last year, Yuan-san went to a conference in Bali with such support. Pay attention to email announcements if you're interested. If you want help on targeting conferences, let me know.
There is also a budget granted to faculty based on the number and kind of students which can be used for student travel to presentations and conferences, but also can be used to acquire other resources (books, software, data, hardware, media -- see Record keeping, below). It's about ¥40,000/student, but you shouldn't consider that an individual budget. Some students won't use it at all, others may use two or three times as much.
Note that to the extent that resources are durable, they're property of the university lent to the laboratory. When you leave, you'll have to return them to the lab.
There is an immense amount of information available on the Internet. Besides the major search engines (Google, Bing, Baidu) there are more specialized ones like Google Scholar. Governments, intergovernmental organizations (like the UN, IMF, and World Bank) provide huge ammounts of macroeconomic and microeconomic data.
There's also a lot of metadata: article reviews in blogs, journal rankings, journal impact factors, etc. You should use these resources when evaluating prior research, but always remember that they're free and not peer-reviewed.
You should be especially careful about free "research" online that you find with (regular) Google: undergraduate and master theses, commercial sources, etc. -- evaluate these very carefully.
Your documents, data, and programs are your research life. It's really important to have backups. One approach is to save your current versions to USB, pretty much every day, and to save "important" versions (certainly anything you present, and maybe weekly backups of data being collected) to something more permanent like CDs (well, really, do you think you're going to produce more than 640MB of product?! -- if you do, go ahead and use DVDs or BDs).
But there's a better way, called version control software. The most popular such software now is called git, and was written by Linus Torvalds who also created the Linux operating system kernel. git has a poor reputation as being hard to use, but that's in use cases where many people are cooperating in developing a single project. For personal use, it's not hard (and there's add-on software that makes it even easier). "git means never deleting your data and saying 'oh shit'!" If you use software development tools like Xcode (Mac) and Eclipse (Java) and maybe Visual Studio (Windows), it's already built in, and it's easy to download git.
With git, you can commit a file (or a whole folder of files) to your repository (archive of past versions of your project) at any time, and then recreate that state exactly at any later time. You can diff the file against any past version to find out what you've done since then, and you can annotate files to find out which lines were changed in which versions. You can use standard utilities to save your whole repository to backup media. You can also push those versions to a repository on the Internet, automatically backing up your project. It compresses the storage, so even keeping hundreds of versions may be less than the storage needed for your current version.
There are even free services such as GitHub and GitLab which may be convenient for backup. However, you must be careful about using their free services: they require that you publish your repository to the whole world with an open source license, and you may not want to do that if you're in the middle of research because somebody else could take your idea and even your programs and data -- completely legally, although that would be unethical. They provide even better services which allow privacy for a reasonable fee, as well. Also, I already have such a repository, and can make it available to students (but I need to make more space on that system).
Get git, you won't regret it if you've got data and documents that change frequently and you need older versions sometimes, but would rather not have them polluting your folders.
Python: easy-to-learn general-purpose programming language, with excellent add-on tools for statistical analysis, database work, natural language processing, and Internet access (eg, "screen-scraping") and publishing (websites), and automating personal data-processing.
The Conda platform from the Anaconda company is probably the most popular way to install an up-to-date (but not bleeding edge) Python system.
R: the premier language for research in new statistical methods. You may prefer "canned" proprietary tools available on Shako workstations like SPSS and EViews though. It's not an easy language.
Jupyter: a notebook system that allows interactive, literate programming which interleaves code, results, and documentation. Most popular with Python and R, but can be used with other software as well. (I'm still learning about this; I'm an Emacs user which provides a similar degree of integration of editing work with computing or programming work, though not in "notebook" form.)
Others: tons and tons.
My advice is to avoid wordprocessors and other proprietary systems if you can, prefer plain-text systems: LaTeX and markdown for text, gnuplot and graphviz for line graphics. Sometimes you must use images, that's OK.
The main advantage of using plaintext is that you can keep a permanent, reliable record of changes you've made and why using git. Although git is perfectly happy to store many versions of a Word document, they compress very poorly, and can't be diff'ed at all as far as I know. (It's theoretically possible, but I don't know of free tools for it.)
Plain text formats are also retargetable to multiple platforms (Mac, Windows, Linux, web) and multiple presentations (web, hardcopy) with options -- if you don't like the particular output of one program you can use a different one, or if you're really serious, you can often fix it yourself. This is much harder with proprietary formats like Word and Excel.
Rules: The library, projector, video camera, printer, and peripherals like CD/DVD/BD drive are free for use in room, but require permission (which is not automatic) for use outside of the room. (Good luch moving the printer! ... That's not an invitation to try!) If you take them to your own desk, they must remain visible on the desk when you're not using them.
Personal resources: If you leave them on the desk, they're available to other students for use in room unless clearly marked as personal to you.
If you break something: Report it to me immediately.