Troubleshoot, Troubleshoot, Troubleshoot!

Time for a new week!

This week started off with our regular Monday meeting. We go around and share what we have been up to over the past week. When it came to our turn, Hans and I shared the progress we had made and mentioned some of the issues we were having. As part of our video series, we will need a presenter…so we asked around to see if anyone might be interested.

This meeting, like many so far, was accompanied with little donut balls, meaty triangles and sugary tea. A nice start to the day in my opinion…but of course I would say that!

From here, it was back on to the project. We are creating a video series teaching bioinformatics and soft transferrable skills. The big issue we first need to address – the microphone. We tried recording some footage last week with the microphones available and the sound quality was quite poor. There were however lots of settings to tinker with and so this is exactly what we did.

Lots of recording. adjusting, sound-checks, post-processing editing…of course followed by much re-recording. We were getting closer to a more professional sound with the microphone set-up we had but it was still a struggle. We were faced with tinny audio that seemed to lack most of its bass. It was an annoying speedbump but not the end of the world. At the very least, we had a microphone which we could use to record the pilot episode while we acquired a more professional microphone for the full video series.

To try to dig deeper in to the microphone issues we were having, we had a skype call to our colleagues back in the UK. We discussed potential solutions, work-arounds, as well as the project in general.

Alongside the extensive troubleshooting fiasco, I set about to create some of the graphical elements for the video series. This included a logo, an icon, animations and titles. After wrestling with the software, I managed to get something that was simple and demonstrated the kind of thing that might be suitable for the project going forward.

This week was also a good chance to learn more of the ins and outs regarding the software and hardware. Its very easy to just gloss over much of the more technical aspects initially but to really understand what it is going on proved to be so helpful. I know understand much more about videography and sound which I am positive will lead to a better final output at the end of this project. The same can be said about much of the software. Before I started, I wouldn’t have had a clue how to use any of the software, let alone what many of the buttons and features did. I now feel a lot more confident with these applications. I’m far from an expert but I do now at least have a much more solid foundation to work with when it comes to using them for the video production.

One of the overall major tasks with this project is to create a user guide. This user guide will contain all the technical information about how to continue producing this video series once we are back in the UK. It will describe all of the hardware, software and video production process. So, this week, I got stuck in to that! We’ve had to face quite a bit of troubleshooting so far but with this guide, hopefully the people who continue this video series after us will be able to jump straight in, after giving this guide a read.

This week, I was able to get stuck in to some proper video editing. To learn more of the intricacies of the software and to also get something useful for the final episode, I set about creating an intro for my training videos. After wresting with software which at first I found to be quite unintuitive, I produced both a short and long intro suitable for my videos….success!

Friday had approached where we were invited to attend a guest seminar entitled “Plant Nutrition Studies Leading to Improved Production of Biomass and Biocoal” delivered by Prof. Toru Fujiwara from the University of Tokyo. It was great to get to hear some cutting-edge science out here and to see the potential real-world benefits from this research.

And so, the weekend was upon us.

Friday night, we embarked upon a journey downtown to attend a French-Ethiopian jazz evening. While a slightly unconventional jazz ensemble, the music was really enjoyable. This music venue was a popular choice for many ex-pats and Kenyan locals alike. The music was filled with rhythm and expression, you just couldn’t help but tap your foot along to the beat (or in the case of Hans, get up and start dancing your heart out right at the front). This was our first venture in to the central business district (CDB), but it certainly wouldn’t be the last.

On Saturday we ventured out to Hells Gate national park. Now despite the slightly off-putting name, Hells Gate is an incredible site of natural landscapes and biodiversity right next to Nairobi. To add to this, it does have some interesting quirks. Firstly, this is a National Park which you can cycle through (one of just two)! Secondly, it’s the site of three geothermal power stations which produce a large portion of Kenya’s renewable energy (for which Kenya is one of the world leaders in). Thirdly, it is also well known on the big-screen. It served as inspiration for the setting of 1994’s The Lion King with many of the key features being modelled in to the movie. As well as this, the 2003 movie Lara Croft Tomb Raider: The Cradle of Life was filmed on location at the park. With stunning scenery like this (below), who can blame them!

We were lucky enough to get an on-foot guided tour through the hells gate gorge (Njorawa), an impressive 24-kilometre-deep ravine carving through the natural landscape. We stumbled up and over rock formations with towering walls either side, it was quite the experience. It sort of cast my mind back to the pod-racing scene from star wars episode I. Sheer cliffs, twist and turns…but alas, no Jawas to pick up the discarded scrap mechanical pieces.

Throughout the gorge, were white markings on some of the stone. It was explained to us that this was due to sulphur. Also dotted throughout the gorge were these waterfalls (both very tiny and much larger). They were incredibly hot! A small water stream dripping down the rockface, we were told, was around 30 degrees Celsius while another, much larger waterfall was a whopping 70 degrees Celsius. Far too hot for me! This water flowed from natural hot water springs heated with geothermal energy. What I really found very cool was that with most of these flowing water sources, they were accompanied with green growth. This was green thermophilic blue-green algae. We were discussing how interesting it would be to do some metagenomic analysis of not just the algae, but of all the life in these water sources. Extremophiles and thermophiles often possess such interesting and unique ways of maintaining survival and are often littered with novel secondary natural metabolites. I guess that was our inner scientists geeking out!

We climbed a steep hill out of the gorge where we were greeting with stunning aerial views of what we have just walked and its location in the national park. From here we browsed and shopped through some market stalls which had been set up by some locals. As we walked along, we got a full view of another marvel of nature. Central tower column. This was a thin, narrow rock column formed through volcanic activity. It stood alone, tall and proud. It was quite impressive and looked to be a good 20/25 meters high.

This wasn’t the only volcanic column though, an arguable more famous one is Fischer tower seen from the eastern entrance. While not as narrow, this column was still impressive. Again, this column formed through volcanic activity. It has been estimated that this column formed 35 million years ago and was named after German explorer Gustav Fischer.        

Sunday night, we spent the evening having dinner, accompanied with some board games, with some new friends in the city. A nice way to wind down ready for another week.

Danny Ward

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[“This work was supported by the Norwich Research Park Doctoral Training Partnership (NRPDTP), by the Biotechnology and Biological Sciences Research Council of the United Kingdom (BBSRC) through the BBSRC-STARS grant with reference BB/R020272/1 awarded for the ABCF Bioinformatics Community of Practice, and by the BecA-ILRI Hub through the Africa Biosciences Challenge Fund (ABCF) program. The ABCF program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida)”

Key personnel/contributors linked to this project:

BecA-ILRI hub (Nairobi) – Dr. Jean-Baka Domelevo Entfellner ¦ Dr. Peter Emmrich ¦ Dr. Wellington Ekaya

John Innes Centre/UEA – JIC Graduate School Office ¦ UEA Internships and Placements team ¦ Hans Pfalzgraf ¦ Danny Ward   

We would like to extend our gratitude to all those listed, along with all others, who contributed and supported towards this project in various capacities – this wouldn’t have been possible without your help]

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