“Stargazing In Upstate NY In September” Article Posted To newyorkupstate.com And syracuse.com

The third article in the series – “Stargazing in Upstate NY in September: Look for more subtle objects on autumn nights” – is available for your reading and critical review at newyorkupstate.com and syracuse.com. I’m pleased to report that we’ve hit our stride with the formatting and content transfer, and I can only hope the star charts make sense in their current forms.

For interested parties, this article also marks the first official mention (to the best of my knowledge) of our upcoming MOST/TACNY/CNYO hosting of International Observe The Moon Night on Saturday, October 8th. Additional details to follow, but expect the observing to happen somewhere around The MOST itself.


Extra-special thanks to Nick Lamendola from the Astronomy Section of the Rochester Academy of Science (image above, taken from the grounds of my new observing stomping grounds at the Farash Center – click for a larger view) for the use of his Perseid composite as the article opener (one of the benefits of being a member of several local clubs is the listserve content – and the many fantastic images that fly by on a weekly basis).

The Methodist Bells And Colin Phils – Highlights Of Sub Rosa Session #32 At Subcat Studios, 21 August 2016

Posting for historical purposes, given the great recording and video that came from the session.


The Methodist Bells (bandcamp facebook) had the pleasure of performing a 3/4 set on Sunday, August 21st at (my first drum teacher, Ron Keck’s) Subcat Studios for Sub Rosa Session #32. Closing for the Bells (well, I think it’s funny) was recently-US-returned-and-immediately-thereafter-Binghamton-bound Colin Phils (bandcamp facebook), who put on a fantastic trio show (and, with one of the wooden USBs in tow, I can say that their previous two albums are excellent as well).


“The band. The band. THE BAND!” Adam, me, Leah, Clem, Jeremy, et Maurice.

Alice In The Sky, featuring an Allis On The Ground

With thanks to Amanda Rogers for organizing, Subcat, The Rebel 105.9 (we don’t get it in Rochester, though), The Syracuse New Times, D.I.T. Records, and my current contributing writer hosters at syracuse.com for making the session and recording possible, a video work-up of “Alice In The Sky” is provided below for your viewing and listening pleasure (courtesy youtube.com).

On day two of an 11-hour jet lag, hadn’t played in a month, stuck behind a poorly-left-ified kit, and still sound good.

The Colin Phils tune “Don Cabs” is included below. I was (admittedly) ready to sneak out early, but ended up staying for the whole set (that’s musician-speak for “great show”).


Our fearless leader Clem Coleman (twitter facebook) was featured in a recent Daily Orange article, in which I make my third (known) appearance in the DO ever since starting at SU in 1994.

Link: dailyorange.com/…/otro-cinco-chef-creates-vintage-inspired-music…

PDF (local, for posterity): 2016sept7_methodistbells_dailyorange.pdf

“Stargazing In Upstate New York” – Links To The First Two Columns At newyorkupstate.com And syracuse.com

Free press all around,

In the interest of aggregation, quick post linking the first two in a new series of astronomy articles on newyorkupstate.com and syracuse.com. There’s an old adage in academia – “You don’t really know something until you can teach it.” To that end, these articles and their associated research prep are great fun and yet another excellent excuse to go out at night and compare the planetarium apps to the real thing (for which both Starry Night Pro and Stellarium are excellent organizational proxies. I’m currently leaning on Stellarium for the imagery because others who might get bit by the astronomy bug can download it for free and follow along. That said, Starry Night Pro is still my workhorse for fine detail as Stellarium continues to develop).


When the article series was first proposed, the goal for the Syracuse Media Group folks was to provide people in upstate some basic information for what was up and about in the night sky – when you step outside, what’s there to find? My hope is to provide the non-observer and novice observer just enough information to whet the appetite, hopefully coaxing readers to take some quality looks and, if all goes well, to seek out their local astronomy club for some serious observing – and learning.

Night sky-gazing in Upstate NY: What to look for in July

– newyorkupstate.com article @ newyorkupstate.com…_look_for_in_july.html

– syracuse.com article @ syracuse.com…_look_for_in_july.html

Introducing the article organization, with first looks, spotting the International Space Station (ISS), moon phases, visible planets, and a constellation-a-month identifier to close it all.

Stargazing in Upstate NY in August: See the Milky Way, Perseid meteor shower

– newyorkupstate.com article @ newyorkupstate.com…_meteor_shower.html

– syracuse.com article @ syracuse.com…_meteor_shower.html

The series started just in time to highlight the Perseid Meteor Shower (and get its first linking to thanks to Glenn Coin’s article as we approached the Perseid peak), then August was chock full of interesting planetary events. The August article was also a first exposure to the issues of episodic astronomy – how to be as minimally referential as possible in any single article to previous articles (which is not easy given how much the search for constellations historically has involved the finding of a bright one to orient observers to a dimmer one).

July hit 78 shares on newyorkupstate.com, August hit 4400 – at that rate, the whole world will see the October article.

Peptide Springiness By Terahertz Spectroscopy – An Upcoming Cover For Angewandte Chemie (And A POV-Ray File For Generating Springs)


From: onlinelibrary.wiley.com/doi/10.1002/anie.201603825/full

Image caption: An approach combining terahertz spectroscopy, X-ray diffraction, and solid-state density functional theory was utilized to accurately measure the elasticities of poly-l-proline helices by probing their spring-like vibrational motions. In their communication (DOI: 10.1002/anie.201602268), T. M. Korter and co-workers reveal that poly-l-proline is less rigid than commonly expected, and that the all-cis and all-trans helical forms exhibit significantly different Young’s moduli.

Article: onlinelibrary.wiley.com/doi/10.1002/anie.201602268/abstract

Continue reading “Peptide Springiness By Terahertz Spectroscopy – An Upcoming Cover For Angewandte Chemie (And A POV-Ray File For Generating Springs)”

More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)

“Stop that!” – George Carlin

If you’ve obtained source code from an academic lab that was last developed some time ago and you spent a whole day installing libraries and symbolic links and redefining variables in your .bashrc and downgrading libraries and redefining paths and have 20 tabs open in your browser that all go to 20 different obscure error discussions on Stack Overflow and it’s late and you’re tired and you think you might not need the program after all if you do a bunch of other workaround things instead – what’s below is for you.

Academics have been developing small code for (nearly) millions of years to make their lives easier – and we all benefit when that code is made available to others (esp. when it helps in data analysis). When that code is a series of perl or python scripts, there’s generally little reason why you should have any run issues. When they call on external libraries or specific tools, generally that information is available in the README somewhere. Generally speaking, there’s no reason why a code shouldn’t work in a straightforward manner when the developer doesn’t make it known that something else needs be installed to make it work.

So, why doesn’t code A work on your linux box? A few possibilities.

Continue reading “More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)”

OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes

UPDATE: 20 May 2016 – With thanks to OrthoDB’s very own Fredrik Tegenfeldt, here’s a more distro-complete fix for the Makefile.rules file.

# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR        = $(BASE_DIR)
CPPFLAGS    += -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS        += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR)
LDFLAGS        += -L$(LIB_DIR)
LDLIBS        += -lbrh

ifeq ($(USE_BOOST_THREAD),1)
LDFLAGS        += -pthread
LDLIBS      += -L$(DIR_BOOST_LIB) -lboost_system -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD) -lpthread

And Happy New Year,

Yet another random Ubuntu-centric bioinformatics aside in the event others run into the same build issues (with errors included below, as you likely googled those first). For those wondering…

The Hierarchical Catalog of Orthologs v8

Orthology (website, download) is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.

The build here was on a fresh installation of 64-bit Ubuntu 14.04 (Trusty Tahr). All of the errors produced come from running on that clean install, meaning you’ll run into dumb errors (like missing build-essential), didn’t-know-we-needed-that errors (boost), and that’s-probbly-an-Ubuntu-oddity errors (with a modified Makefile.rules file with explicit boost calls linked to below; I suspect the developers are working on a non-Ubuntu distro).

Continue reading “OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes”

Some Recent WordPress Theme Hacking Issues (Mass Emails To Non-Existent Domain Name Addresses) And A Couple Of Things To Look For

I’ve spent the past few weeks making several new email client filters each day, with subject lists that look like the following:

Saturday and Sunday Only! Today’s Special Buy of the Day!

One day sale event – today only, [ insert date here ]

[ insert name here ], check out this weeks specials – up to 75% off on selected items

[ Insert name here ], 10% discount for Brand or Generics for purchases placed before [ insert date here ]

We appreciate your past business with us

[ insert name here ], some of your items are back in stock now – complete your order today

[ insert date here ] deals and savings from your supplier

Continue reading “Some Recent WordPress Theme Hacking Issues (Mass Emails To Non-Existent Domain Name Addresses) And A Couple Of Things To Look For”

Private Internet Access, OpenVPN (2.3.2), and Ubuntu 14.04 (.2 LTS) – Yet Another Reported Way To Get Them Working (And The Only One That Works For Me)

Update: 17 May 2016 – Doesn’t happen often and is always nice to see. Thanks to Lucas Nell (on 26 April – that’s my bad) for taking one additional step out of the whole process with the script below. Simply replace “[put-your-password-here]” with your actual password (and no brackets), same the below as some_name.script (or whatever), chmod +x some_name.script to make it official, and you’re good to go to make the additional mod.

sudo -s

cd /etc/NetworkManager/system-connections

export pwd="\n[vpn-secrets]\npassword=[put-your-password-here]"

for f in PIA*
  sed -i 's/password-flags=1/password-flags=0/g' "${f}"
  echo -e "${pwd}" >> "${f}"


If you sign up for an account with Private Internet Access (and this may go for some other VPN providers as well) and follow the only prominent Ubuntu link (12.04) in the Support Section (www.privateinternetaccess.com/pages/client-support/ubuntu-openvpn), you’ll be taken to a reasonably straightforward 9-step process that walks you through the OpenVPN setup – from the install_ubuntu.sh script download to the selection of PIA-points (I just made that up) in your Network Manager GUI (that radial wifi icon or arrows in the upper-right corner).

That is, for Ubuntu 12.04.

The Problem

If you try this in Ubuntu 14.04, everything more-or-less looks and runs the same way. That said, when you try to connect to a PIA-point in the Network Manager, nothing happens. Your wifi radial doesn’t change, flash, or provide any indication that something has gone right or wrong. More importantly (to the lack of feedback, anyway), you are not asked for your PIA password (having put in your username in the install process). This lack of password requesting turns out to be the real kicker (and diagnostic for the fix presented down below).

Continue reading “Private Internet Access, OpenVPN (2.3.2), and Ubuntu 14.04 (.2 LTS) – Yet Another Reported Way To Get Them Working (And The Only One That Works For Me)”

Led Astray By (A) Photon – WordPress, Jetpack, and The Perils Of Embedded Clear Sky Charts (And Other)

A re-post from the CNY Observers website (www.cnyo.org).

Greetings fellow astrophiles,

CNYO has been anticipating our first observing session at Beaver Lake for this year, with the first of our two Spring dates (April 23rd) already clouded/snowed out. The forecast for April 30th hadn’t looked too much better based on Monday estimates, leaving us to wonder if attendees would be stuck indoors with a lecture instead of outdoors with the rest of the universe.

I woke up early on the 30th to blue skies and a very bright Sun, certainly already exceeding the expectations of the past few days. But what of the afternoon and evening?

As I am prone to do on the day of an observing session, I headed right for the CNYO Cheat Sheet, where one can find the sky conditions for a large part of Central New York in the form of several Clear Sky Charts (CSCs – and, based on the different cloud cover at different locations, even begin to piece together how the skies at your location may change). The morning’s CSCs are shown in the image below.

Continue reading “Led Astray By (A) Photon – WordPress, Jetpack, and The Perils Of Embedded Clear Sky Charts (And Other)”

CNYO Observing Log: The Winter Of Lovejoy – Green Lakes, Jamesville Beach, And New Moon Telescopes HQ – January 9 to 14, 2015

A re-post from the CNY Observers website (www.cnyo.org).


Caption: Comet Lovejoy imaged on January 10th by the ever-impressive CNY astrophotographer Stephen Shaner. From his CNYO Facebook Group post: Last night was the first in over three months it was clear enough to shoot, but it worked out well because Comet Lovejoy is at its peak. Here’s a quick process of about 40 minutes of exposures between 8-9 PM as it crossed the meridian. FOV is roughly three degrees. Distinct pale green coma in the eyepiece but unable to make out a tail or see it naked eye.

The 2015 skies are going to be full of comets. Well, at least six, to be exact, that will be either naked eye- or binocular-visible. That’s still quite a few to those keeping track! The amateur astronomy community has taken heroic efforts to scientifically identify and track new comets in the last, say, 400 years. The rise of, for instance, the Panoramic Survey Telescope & Rapid Response System (or panSTARRS) as a method for finding and tracking both comets and near-earth asteroids (or, lumped together, “objects,” for which you might hear the abbreviation “NEOs”) has greatly increased the number of accounted-for fuzzy objects in our fields of view (and provided us a giant leap in our existential risk assessment infrastructure to boot). Quite simply, we’ve more + better eyes on the skies, meaning we’re bound to continue to find more and more comets and asteroids. You can even subscribe to NASA twitter feeds that announce the passing-by of these hopefully passers-by (see @AsteroidWatch and @NasaNEOCam).

Continue reading “CNYO Observing Log: The Winter Of Lovejoy – Green Lakes, Jamesville Beach, And New Moon Telescopes HQ – January 9 to 14, 2015”