Tag Archives: reference manager

(accepted) Topic Modeling: An Approach for Research Design

The following abstract is accepted for the upcoming 6th International Conference on Educational, Management, Administration and Leadership (6th ICEMAL 2016) will be held on August 28, 2016 in Bandung, Indonesia. Below I’ve updated with pre-event video presentation.


Topic Modeling: An Approach for Research Design

Dasapta Erwin Irawan (a*), Adhi Priyambodho (b)

a) Faculty of Earth Sciences and Technology,
Bandung Institute of Technology
Jalan Ganesha 10, Bandung 40132, Indonesia

b) Faculty of Water Resources,
TU Delft, The Netherlands


Research design has been a major problem for early career researcher, especially PhD students. This paper discusses new approach to assist a researcher choosing their research topic based on previous papers/studies. Here we use open source tools (Vosviewer and Zotero reference manager) to visualize research topic under keywords “groundwater Jakarta” from close to 256 papers harvested from Google Scholar and Crossref scientific database. Using this approach we can identify the change of main research issues in groundwater resources from the 70s to date. We also see the research flow path during the period and determine new interesting subtopics. Based on the result we believe that this technique is applicable for postgraduate students

Keywords: topic modeling, data visualization, reference manager

Topic: Internet technologies in Education

Full paper and other resources (datasets, images) are stored here, and the slide v1.0 is already available on SpeakerDeck.



Reference Management Course


(image from: boxyblogs.com)



KK Geologi Terapan dan Comlabs menyelenggarakan:

Mini Workshop

Memulai menulis dari daftar pustaka: bagaimana mengelola referensi

Hari/tanggal: Rabu, 28Jan2015
Jam: 13-16
Tempat: R. Hilmi Panigoro, GL lt 2

Terbuka utk umum. Tempat terbatas.

slide: http://goo.gl/n1qHcq

Software: http://www.zotero.org

Download dan install:

zotero app, connector to firefox, connector to MsWord/LibreOffice.

Diharapkan bawa laptop dgn baterai terisi penuh.

View on Path

Attention to participants: Intro to R and Reference Management


(image from: writingclassesforkids.com)

For Intro to R and Reference Management course participant.

Be sure to download and install all the required softwares prior to enter the class.

1) R base from cran.r-project.org
2) R Studio from rstudio.com
3) zotero app, zotero addins for firefox, zotero addins for MsWord/LibreOffice from zotero.org

See you later in class.

View on Path

WTF: More on reference manager Zotero


(image from: wiki.ubc.ca)

Dear friends,

I’ve been posting my research plan for 2015 in various medias, so that my students, or any other students in Indonesia could read it and participate. I’ve got many responses. And the following post is my comment. I’ll make the translation later on.

— In Indonesian —

Kalau anda berminat pertama yg mau saya share adalah ilmu reference manager untuk membuat daftar pustaka:
  1. Googling software Zotero;
  2. Download zotero dan juga add-on untuk Microsoft Word (MsW) atau LibreOffice (LO) dan Firefox (kalau anda pakai Firefox);
  3. Googling BibTex citation info. Ini penting karena ini file yang menyimpan info identitas tiap paper, buku, peta yang kita rujuk (cite).
  4. Untuk tutorial format video, tautan screen cast di youtube berikut sangat membantu: http://goo.gl/7QRzsc

Jadi biasakan tiap download pdf paper atau apapun, cari atau download juga BibTex citation infonya untuk “disedot” (import) dengan Zotero.

 Dengan reference manager (EndNote, Mendeley, Zotero, dll), in this case we’ll be using Zotero (free and opensource), kita hanya perlu berhenti di tempat yang tepat, memilih paper yang kita cite, Daftar Pustaka (Bibliography) akan dibuat secara otomatis oleh Zotero. Mendeley is also free (but not open source), so the choice is yours.
Selain menggunakan software eksternal, anda juga bisa menggunakan fasilitas reference manager internal MsW atau LO. Outputnya sama, tapi MsW tidak bisa membuka atau import BibTex citation info, jadi anda harus memasukkan judul, penulis, dll satu-satu. Tapi masalah itu sudah diselesaikan dengan mendownload dan menginstalasi addon Zotero untuk ms word atau libreoffice. Akan muncul icon dan menu tambahan untuk menyisipkan citation di posisi yang kita inginkan.
Bagi yang ingin mencoba fasilitas internal MsW atau LO, saya sudah buatkan tutorialnya empat tahun yang lalu di blog saya di FITB (http://goo.gl/QWj2At).

— In English —

If you are interested, the first thing I want to share with you will be how to use reference manager to help you manage you and make citation lists. So what I need you to do are:
  1. Googling Zotero;
  2. Download zotero and also its add-on for Microsoft Word (MsW) or LibreOffice (LO) and its Firefox extension (kalau anda pakai Firefox). For those of you who use Chrome, in my experience, the extension is not fully working;
  3. Googling BibTex citation info. This file stores the citation info of your papers, books, maps, or whatever that you want to cite.
  4. You might find this video tutorial useful.

From now on, don’t forget to download the BibTex citation info after or before you download a pdf. In fact, make it as a habit. This “*.bib” file will be later on imported to Zotero.

Using a reference manager (EndNote, Mendeley, Zotero, dll), in this case we’ll be using Zotero (free and open source), all you have to do is stop whereever you need to cite, select the paper to cite, then the bibliography (reference list) will be automatically synced by Zotero. Mendeley, however, is also free (but not open source), so the choice is yours.
Instead of using external software, you have another choice to use the internal referencing facility in you word processor (WP), either MsW or LO. The output will be the same, but both WP can’t read any formats of citation info (BibTex, RIS, RefWorks, EndNote, etc). So you will need to input the info (title, author, year, etc) one by one. But that has been solved by downloading and installing Zotero add-on in to your WP. You may expect additional menus and icons from the add-on.

WTF: Merging duplicated citation info Zotero

With your long list of citation info over the years, there might be chances of duplicated citation info. Reference manager is very handy in dealing with this problem. The following picture is how you do it in Zotero.

Just go to the “Duplicates” tab in your left side pane.  It will detect duplicated entries in you collections or libraries. Then click on the series of duplicates then hit “Merge items” on the right side pane.

Merging duplicated citation info in Zotero
Merging duplicated citation info in Zotero

WTF: Reference manager: citation info

Skip this post if you’re an experience (academic) writer. That will save your time. :-). pdf or this post is available at Academia.edu.

Ever heard of reference manager? If you’ve heard or used EndNote (a long widely known software owned by Thomson Reuters), then you must know what is reference manager is. Basically it stores your references. No matter what kind of references you have: physical books, microfilms, maps, educational movies, or pdfs, kindles, websites, personal communication etc. It generates an archives of the materials for you. Actually, it saves the citation info of the materials.

What is citation info?

it is a set of metadata that glued to your materials. The citation info is the ID of any references you have. So you won’t mixed them up. Say you have a pdf file containing an article from a journal. If you hit “File”, “Properties” in your pdf viewer, you would see the informations related to the file, like: filename, title, author, year, journal, vol, no, etc. You are looking to the citation info of the pdf file.

Where to get such info?

You might want to read the slide on my other post Open Source Writing. Generally, you can get it from any button or menu called: “cite” or “export citation”.

Is citation info in form of a file?

Yes, it is a file with many kinds of extension:

  • *.bib for BibTeX format
  • *.ris for RIS format
  • *.enl for EndNote format

You can even save the abstract of your chosen paper in the citation info.

Is it important to have citation info?

Yes it is. The first thing is that every papers, assignments, reports that you are working on, must need references at certain level. Your references will add up quickly as time goes by. Next time you check, your list might containing hundreds or maybe thousands of materials (pdfs etc). At that time you would think “I should have stored the citation infos and used reference manager, when I started building this pile”.

Next: Reference manager (2): EndNote?

Citation info from Zotero