
Researching the research
By Horacio Pérez-Sánchez

Researching the researchDec 17, 2021

13. The Archaeology of Language: Place Names and Endangered Languages in the Search for the Origins
In today's episode, historical linguists and language documentarists Francesco Perono Cacciafoco (Associate Professor at Xi'an Jiaotong-Liverpool University, https://www.xjtlu.edu.cn/en/study/departments/school-of-humanities-and-social-sciences/department-of-applied-linguistics/department-staff/academic-staff/staff/francesco-perono) and Shiyue Wu (Linguistics' major at Xi'an Jiaotong-Liverpool University) discuss their research on Historical Linguistics and endangered and undocumented languages. Francesco provides us with background on his work reconstructing, documenting, and analyzing place names (toponyms) in languages from all over the world. He explains how place names can give insights into prehistoric languages, since they are more stable over time than other words. His recent book "Place Names: Approaches and Perspectives in Toponymy and Toponomastics", published by the Cambridge University Press (https://bit.ly/3NZc2I2), aims to be a comprehensive guide to toponymic research, the first academic handbook on Toponymy ever published in single volume.
The process of analyzing place names involves documentary research and etymological reconstruction, comparing toponyms among related languages, belonging to the same language families, recovering possible earlier 'proto-forms', and giving back to those special names their often long-forgotten morphological roots and original meanings. Challenges include to deal with unsolvable prehistoric / ancient place names and with toponyms connected with 'itinerant' and undocumented oral traditions and language contact in Aboriginal contexts.
Shiyue shares how she conducts her Language Documentation fieldwork, interacting with indigenous speakers to understand and record words, names, grammatical elements, concepts, and cognitive processes behind their languages. She is, currently, studying number systems and counting among the Abui, Kula, and Sawila peoples from Alor Island (Southeastern Indonesia), documenting and safeguarding their languages and discovering cultural connections, naming processes, and oral traditions.
The two linguists explain also the use of computational tools in their attempts to better understand and, ultimately, decipher undeciphered ancient writing systems, discovering the languages that they 'hide'. Their work focuses on Linear A, a Bronze Age script from the island of Crete, in the Aegean Sea, 'concealing' the so-called (unknown) Minoan language, and on the writing system of the Singapore Stone, a puzzling, fragmentary epigraph from the Lion City, in Southeastern Asia, which carries a script that is unique in the world (never found in any other inscription).
Shiyue's and Francesco's main goals are the reconstruction of prehistoric languages, following the 'dream' of 'giving back the voice' to our ancient ancestors who had not the technology of writing yet, and to document endangered and undocumented languages and cultures from around the world, to prevent their (often very high) risk of extinction and disappearance and to safeguard them for the future generations.
Overall, the episode provides an insightful look at the linguistic detective work involved in reconstructing, analyzing, and documenting place names, oral traditions, and endangered indigenous languages and, ultimately, at what Historical Linguistics and Language Documentation are. The researchers aim to preserve linguistic diversity and study how language evolves over time and intersects with culture, history, and thought.
Shiyue and Francesco can be contacted at Shiyue.Wu21@student.xjtlu.edu.cn and Francesco.Perono@xjtlu.edu.cn.
Links to some of the commented papers:
https://www.sciencedirect.com/science/article/abs/pii/S0024384116301784
https://www.mdpi.com/2077-1444/9/7/211
https://geografie.uvt.ro/wp-content/uploads/2015/06/08_III_CAC_2.pdf
https://brill.com/view/journals/ow/1/1/article-p1_1.xml?language=en

12. How can you be more productive in your research using consolidated apps: Akiflow
If you want to go far in your research it is crucial to be productive and nowadays there are many interesting productivity apps and systems that you can use for that. But the problem is that there are many! And it is very difficult to find one that suits all your needs. Another problem in this regard is that when you collaborate with other researchers they will probably use other productivity applications, so at the end you spend a lot of time switching between productivity and time management applications.
Today's interviewee has a solution for this! Nunzio Martinello:
https://www.linkedin.com/in/nunziomartinello/?originalSubdomain=in
is the CEO of Akiflow, and they developed Akiflow proposing the idea of consolidated apps. Akiflow allows you to have a central dashboard with calendar which allows you to integrate and sync tasks from many different systems such as gmail, Trello, Todoist, etc, and Zapier, which allows you an even higher number of integrations.
So today we had Nunzio in the podcast and he gave some very interesting explanations about Akiflow and answered our questions. We really recommend you to use it:
If you want to continue discussion about this episode and in general about the themes we talk in our podcast (how research is made, how to do it more efficiently, interviews to researchers, etc) then join our discord community at:
PS: Background music "Let the sunshine" from "Keep Calm and Podcast":
https://pod.co/keep-calm-and-podcast

11. Making it Rain: Cloud-Based Molecular Simulations for Everyone with Pablo Arantes in our Journal Club
First journal club episode from our Structural Bioinformatics and High Performance Computing (BIO-HPC) community which you can joint at:
where we discussed about the paper "Making it Rain: Cloud-Based Molecular Simulations for Everyone":
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00998
with its first author, Pablo Arantes from University of California Riverside:
https://www.researchgate.net/profile/Pablo-Arantes
It would be great to have you in our next Journal Club!
PS: Background music "Let the sunshine" from "Keep Calm and Podcast":

10. Molecular Dynamics with Hugo Verli from UFRGS, Brazil
In this episode we focus around the computer simulation technique Molecular Dynamics (MD), which allows the study of the dynamics of systems of biological relevance. For such purpose we have the pleasure to interview Prof. Hugo Verli from UFRGS, Brazil:
https://scholar.google.com/citations?user=fB-31L4AAAAJ&hl=es
and you can contact via email in case of questions at:
hverli@cbiot.ufrgs.br
or
hugoverli@gmail.com
We also talked about his research career, his views about the research process and many other interesting topics.
If you want to continue discussion about this episode then join our discord community at:
https://discord.gg/3dN7pQNWAk

9. Nanotechnology and research in graphene with Romain Danneau from Karlsruhe Institute of Technology
Interview with key topics in nanotechnology and graphene research with Romain Danneau from Karlsruhe Institute of Technology:
https://www.int.kit.edu/1244_romain.danneau.php
you can contact him directly through his email address (link below) if you have questions about his very interesting research.
We also talked about his research career, his views about the research process and how to manage a research group.
If you want to continue discussion about this episode then join our discord community at:
https://discord.gg/3dN7pQNWAk

8. Why multitasking can be efficient (I): multiple difficult projects or creative processes
This is an episode in the productivity for researchers series. Today I explain why multitasking can be very efficient or perhaps the only way to work on multiple difficult research projects or creative processes, taking advantage of our subconscious mind to find solutions or unblock us.
Contact me at: horacio (at) horacio-ps.com if you want to join our webinar where I will live and interactively explain the technique.
If you want you can continue it here in our public Telegram group at:
https://t.me/researching_research
Thanks for listening!
PS: Image taken from:
https://thenounproject.com/term/multitasking/995438/

7. Research groups vs startups
This is the first episode about startups, where I comment main similarities and differences between research groups in academia and startups. It is based on a very interesting blog post from Charl Both, from Delft University:
https://cpbotha.net/2012/07/24/startups-vs-academic-research-groups-fight/
At the end of the episode there are some open questions for discussion. If you want you can continue it here in our public Telegram group at:
https://t.me/researching_research
Thanks for listening!
BTW: Spanish version of the episode:
PS: Image taken from:
https://pixabay.com/illustrations/businessman-startup-success-arrow-2330853/

6. Modeling water in biomolecular systems with Maria Bzówka from Tunneling group, Silesian University of Technology
Maria Bzówka is a PhD student from Tunneling group, Silesian University of Technology in Gliwice, Poland, working on developing computational methods and their application to biomolecular systems. She visited our research group in September, and we learnt a lot of things from her! In today’s show, we talked about her career, research and views about science
If you want to know more about her, please check the following websites about:
a) her research group:
https://twitter.com/tunnelinggroup
b) the software Aquaduct:
https://academic.oup.com/bioinformatics/article/36/8/2599/5682414
https://www.livecomsjournal.org/index.php/livecoms/article/view/v2i1e21383
https://www.youtube.com/watch?v=3HKtINTemsI
c) her COVID papers:
https://www.mdpi.com/1422-0067/21/9/3099/htm
https://www.mdpi.com/1422-0067/22/4/2065/htm
d) her hsEH Review:
https://www.sciencedirect.com/science/article/pii/S135964462100252X
You can contact her at:
m.bzowka@tunnelinggroup.pl or maria.bzowka@polsl.pl
https://twitter.com/BzowkaMaria
The recording of this episode was performed at UCAM thanks to the audio recording and edition assistance of UCAM’s Unit for Scientific Culture and Innovation (Unidad de Cultura Científica e Innovación). Special thanks to Francisco Ruiz.
And last but not least, you can continue the discussion about the show in our Telegram group:

5. How to explore research ideas just recording a podcast episode
This is the second episode about productivity hacks for researchers, recorded on the street, in which I explain how to explore (and develop new )research ideas just recording a podcast episode.
If you want to get more information about all these steps or are interested on my research consultancy services, you can contact me at
horacio (at) horacio-ps.com
or:
https://horacio-ps.com/en/principal-english/
Finally, you can engage in further discussions about the podcast episodes in our public Telegram group with other users at:
https://t.me/researching_research
Thanks for listening!

4. How to (we) perform computational drug discovery (I): Blind docking
In today's episode I introduce one of the ways we can use computers in order to discovery new drugs. For that I talk about the necessity of multidisciplinary research between structural bioinformatics, high performance computing, and computational drug discovery, just to name a few. Next I explain the Virtual Screening (VS) technique idea and how it is divided into SBVS and LBVS. Focusing in SBVS I explain what a molecular docking simulation is and how a database is processed using it to prioritise compounds for experimental testing. Nevertheless molecular docking can be vastly improved with the Blind Docking (BD) technique and implementation we have developed in our group, BIO-HPC at UCAM, and which is called Achilles Blind Docking server:
https://bio-hpc.ucam.edu/achilles/
this technique is also implemented in our GPU software METADOCK 2:
https://academic.oup.com/bioinformatics/article-abstract/37/11/1515/5711286?redirectedFrom=fulltext
and here I mention two key publications that have used our BD technique:
https://www.science.org/doi/10.1126/sciadv.aba6617
https://www.nature.com/articles/s41589-019-0278-6
And last but not least, you can continue discussion in our Telegram group:
https://t.me/researching_research

3. How the apps installed on your smartphone can influence your productivity as researcher
If you want to get more information about all these steps or are interested on my research consultancy services, you can contact me at horacio (at) horacio-ps.com or:
horacio-ps.com/en/principal-english/
Finally, you can engage in further discussions about the podcast episodes in our public Telegram group with other users at:
https://t.me/researching_research
Thanks for listening!

2. Intro to research grants calls
This is the first episode about research grants in which I introduce what research grants are and how are grant calls usually structured. I talked about:
- How research grant calls are structured
- Advice for the preparation of documents
- The reality of rejection
- Resiliency and feedback
If you want to get more information about all these steps or are interested on my research consultancy services, you can contact me at horacio (at) horacio-ps.com or:
https://horacio-ps.com/en/principal-english/
Finally, you can engage in further discussions about the podcast episodes in our public Telegram group with other users at:
https://t.me/researching_research
Thanks for listening!

1. Structural bioinformatics, scientific career path and advice for PhD students
In this episode I was recently interviewed by Eva Lantsoght and Rico Massa in their podcast PhD Talk:
https://www.evalantsoght.com/podcast.html
where we talked about:
- My scientific career
- How structural bioinformatics and supercomputing works
- Advice for PhD students
- General productivity tips
You can contact me at horacio (at) horacio-ps.com
and you can engage in further discussions about the podcast episodes in our public Telegram group at:
https://t.me/researching_research
Thanks for listening!

Introduction and podcast trailer
First and introductory episode of the podcast in which I briefly explain what the podcast is about and what I think you can expect from it, how it will be recorded, produced and organised, and how to you can give feedback and engage in further discussions.