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Finance perspective : Business School Life
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# Finance perspective

Author Message
Director
Joined: 18 Dec 2007
Posts: 983
Location: Hong Kong
Concentration: Entrepreneurship, Technology
Schools: Hong Kong University of Science and Technology (HKUST) - Class of 2010
Followers: 12

Kudos [?]: 134 [0], given: 10

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27 Mar 2008, 07:36
So , i attended a HKUST alumni event tonight. Quite fortunate, i happen to be in Beijing (on business), and they arranged a celebratory party for their rank in FT (17th) so i was able to join them. One of their professors (specialises in risk management and is an ex-banker) was telling us about the finance job market (in Hong Kong). His basic forecast is that employment in CDOs will be hit and there will be cuts, but he also believes that PE will generally be untouched.

Among the Alumni was the VP of the strategy planning of an IB, (Beijing branch), and he was collecting up a lot of this years HKUST intakes business cards as he was getting ready to prepare for internships for next year. credit crunch has had no impact in their internship hunt in China.

Finally the other interesting thing is the student run funds, they were explaining how they were trying to set it up and probably try to emulate the Darden model. The money is provided by alumni sponsors, is overseen by the alumni, but run by the students. They prefer to have a mix of students who have managed funds before and students who have a high interest in this area. The alumni will review the investment policies the students create before giving a green light.

Anyhow, im not interested in going into finance, so the details here is only what i could understand (most of the talk was done in Mandarin and I don`t really understand it so much)
VP
Joined: 09 Jan 2007
Posts: 1045
Location: New York, NY
Schools: Chicago Booth Class of 2010
Followers: 10

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09 Apr 2008, 13:44
In London things a pretty ugly from what I've heard...

Some Hedge Funds are going down, and also some PE's and small IM firms really getting hard times.

Yesterday I went to a presentation of a Economist from Calyon (Group Credit Agricole) and he is VERY VERY pessimistic, he said that we may see 4Q of recession in USA. I'd be skeptical, but last year in may I saw the same guy's presentation and he called the scenario we are all seeing right now, I can send his name through a PM.

I'm really bearish (and so is my bank) and we keep buying Treasuries on dips (I'm an Fixed Income and Credit Trader ). This year so far has been really good for us, but it's sad because it's good because the market is a mess and we've been pessimistic. The problem is that the volatility is SO HIGH that even with small exposures the return (or the damage) is VERY HIGH.

Nick_sun sent me an article with changes at the HSMP program in UK, let me find it and I post it later if he doesn't.
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Re: Finance perspective   [#permalink] 09 Apr 2008, 13:44
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40m QIL Cryo_Lab CTN SUS_Lab TCS_Lab OMC_Lab CRIME_Lab FEA ENG_Labs OptContFac Mariner WBEEShop
 40m Log, Page 325 of 327 Not logged in
ID Date Author Type Category Subject
15145   Thu Jan 23 15:32:42 2020 gautamConfigurationComputersMegatron: starts up grade

The burt snapshotting is still not so reliable - for whatever reason, the number of snapshot files that actually get written looks random. For example, the 14:19 backup today got all the snaps, but 15:19 did not. There are no obvious red flags in either the cron job logs or the autoburt log files. I also don't see any clues when I run the script in a shell. It'll be good if someone can take a look at this.

15150   Thu Jan 23 23:07:04 2020 JonConfigurationPSLc1psl breakout board wiring

To facilitate wiring the c1psl chassis and scripting loopback tests, I've compiled a distilled spreadsheet with the Acromag-to-breakout board wiring, broken down by connector. This information is extractable from the master spreadsheet, but not easily. There were also a few apparent typos which are fixed here.

The wiring assignments at the time of writing are attached below. Here is the link to the latest spreadsheet.

15158   Mon Jan 27 14:01:01 2020 JordanConfigurationGeneralRepurposed Sorenson Power Supply

The 24 V Sorenson (2nd from bottom) in the small rack west of 1x2 was repurposed to 12V 600 mA, and was run to a terminal block on the north side of 1X1. Cables were routed underneath 1X1 and 1X2 to the terminal blocks. 12V was then routed to the PSL table and banana clip terminals were added.

15159   Mon Jan 27 18:16:30 2020 gautamConfigurationComputersSluggish megatron?

I've also been noticing that the IMC Autolocker scripts are running rather sluggishly on Megatron recently. Some evidence - on Feb 11 2019, the time between the mcup script starting and finishing is ~10 seconds (I don't post the raw log output here to keep the elog short). However, post upgrade, the mean time is more like ~45-50 seconds. Rana mentioned he didn't install any of the modern LIGO software tools post upgrade, so maybe we are using some ancient EPICS binaries. I suspect the cron job for the burt snapshot is also just timing out due to the high latency in channel access. Rana is doing the software install on the new rossa, and once he verifies things are working, we will try implementing the same solution on megatron. The machine is an old Sun Microsystems one, but the system diagnostics don't signal any CPU timeouts or memory overflows, so I'm thinking the problem is software related...

 Quote: The burt snapshotting is still not so reliable - for whatever reason, the number of snapshot files that actually get written looks random. For example, the 14:19 backup today got all the snaps, but 15:19 did not. There are no obvious red flags in either the cron job logs or the autoburt log files. I also don't see any clues when I run the script in a shell. It'll be good if someone can take a look at this.
15164   Tue Jan 28 15:39:04 2020 gautamConfigurationComputersSluggish megatron?

There were a bunch of medm processes stalled on megatron (connected with screenshot taking). To see if they were interfering with the other scripts, I killed all of the medm processes, and commented out the line in the crontab that runs the screenshots every 10 mins. Let's see if this improves stability.

15167   Tue Jan 28 17:36:45 2020 gautamConfigurationComputersLocal EPICS7.0 installed on megatron

[Jon, gautam]

We found that the caput commands were taking much longer to execute on megatron than on pianosa (for example). Suspecting that this had something to do with the fact that megatron was using EPICS binaries from the shared NFS drive which were compiled for a much older OS, I installed the latest stable release of EPICS on megatron. The new caput commands execute much faster. I also added the local EPICS directory to the head of the $PATH variable used by the MC autolocker and FSS Slow scripts, so that they use the new caput command. But mcup is still slow - maybe my new path definition isn't picked up and it is still using the NFS binaries? To be looked into...  Quote: There were a bunch of medm processes stalled on megatron (connected with screenshot taking). To see if they were interfering with the other scripts, I killed all of the medm processes, and commented out the line in the crontab that runs the screenshots every 10 mins. Let's see if this improves stability. 15168 Tue Jan 28 19:12:30 2020 JonConfigurationPSLSpare channels added to c1psl chassis After some discussion with Gautam, I decided to build more spare channels into the new c1psl machine. This is anticipation of adding new laser and ISS channels in the near future, to avoid having to disconnect the installed chassis and pull it out of the rack. The spare channels will be wired to DB37M feedthroughs on the front side of the chassis, with enough wire length to be able to pull the breakout boards out of the front to reconfigure their wiring as needed (e.g., split off channels onto a separate connector). To have enough overhead, this will require installing 1 additional ADC unit (XT1221) and 1 additional DAC (XT1541). We have enough spare BIO channels among the existing units (both sinking and sourcing). This will give us: • 13 spare ADC channels • 14 spare DAC channels • 16 spare sinking BIO channels • 12 spare sourcing BIO channels The updated c1psl chassis wiring assignments are attached. It adds 4 new DB37M connectors for the spare channels (highlighted in yellow) and fixes one typo Jordan found while wiring today. The most current spreadsheet is available here. 15421 Mon Jun 22 10:43:25 2020 JonConfigurationVACVac maintenance at 11 am The vac system is going down at 11 am today for planned maintenance: • Re-install the repaired TP2 and TP3 dry pumps [ELOG 15417] • Incorporate an auto-mailer and flag channel into the controls code for signaling tripped interlocks [ELOG 15413] We will advise when the work is completed. 15424 Mon Jun 22 20:06:06 2020 JonConfigurationVACVac maintenance complete This work is finally complete. The dry pump replacement was finished quickly but the controls updates required some substantial debugging. For one, the mailer code I had been given to install would not run against Python 3.4 on c1vac, the version run by the vac controls since about a year ago. There were some missing dependencies that proved difficult to install (related to Debian Jessie becoming unsupported). I ultimately solved the problem by migrating the whole system to Python 3.5. Getting the Python keyring working within systemd (for email account authentication) also took some time. Edit: The new interlock flag channel is named C1:Vac-interlock_flag. Along the way, I discovered why the interlocks had been failing to auto-close the PSL shutter: The interlock was pointed to the channel C1:AUX-PSL_ShutterRqst. During the recent c1psl upgrade, we renamed this channel C1:PSL-PSL_ShutterRqst. This has been fixed. The main volume is being pumped down, for now still in a TP3-backed configuration. As of 8:30 pm the pressure had fallen back to the upper 1E-6 range. The interlock protection is fully restored. Any time an interlock is triggered in the future, the system will send an immediate notification to 40m mailing list. 👍  Quote: The vac system is going down at 11 am today for planned maintenance: Re-install the repaired TP2 and TP3 dry pumps [ELOG 15417] Incorporate an auto-mailer and flag channel into the controls code for signaling tripped interlocks [ELOG 15413] 15425 Tue Jun 23 17:54:56 2020 ranaConfigurationVACVac maintenance complete I propose we go for all CAPS for all channel names. The lower case names is just a holdover from Steve/Alan from the 90's. All other systems are all CAPS. It avoids us having to force them all to UPPER in the scripts and channel lists. 15446 Wed Jul 1 18:03:04 2020 JonConfigurationVACUPS replacements I looked into how the new UPS devices suggested by Chub would communicate with the vac interlocks. There are several possible ways, listed in order of preference: • Python interlock service directly queries the UPS via a USB link using the (unofficial) tripplite package. Direct communication would be ideal because it avoids introducing a dependency on third-party software outside the monitoring/control capability of the interlock manager. However the documentation warns this package does not work for all models... • Configure Tripp Lite's proprietary software (PowerAlert Local) to send SYSLOG event messages (UDP packets) to a socket monitored by the Python interlock manager. • Configure the proprietary software to execute a custom script upon an event occurring. The script would, e.g., set an EPICS flag channel which the interlock manager is continually monitoring. I recommend we proceed with ordering the Tripp Lite 36HW20 for TP1 and Tripp Lite 1AYA6 for TP2 and TP3 (and other 120V electronics). As far as I can tell, the only difference between the two 120V options is that the 6FXN4 model is TAA-compliant. 15465 Thu Jul 9 18:00:35 2020 JonConfigurationVACUPS replacements Chub has placed the order for two new UPS units (115V for TP2/3 and a 220V version for TP1). They will arrive within the next two weeks.  Quote: I looked into how the new UPS devices suggested by Chub would communicate with the vac interlocks. There are several possible ways, listed in order of preference: Python interlock service directly queries the UPS via a USB link using the (unofficial) tripplite package. Direct communication would be ideal because it avoids introducing a dependency on third-party software outside the monitoring/control capability of the interlock manager. However the documentation warns this package does not work for all models... Configure Tripp Lite's proprietary software (PowerAlert Local) to send SYSLOG event messages (UDP packets) to a socket monitored by the Python interlock manager. Configure the proprietary software to execute a custom script upon an event occurring. The script would, e.g., set an EPICS flag channel which the interlock manager is continually monitoring. I recommend we proceed with ordering the Tripp Lite 36HW20 for TP1 and Tripp Lite 1AYA6 for TP2 and TP3 (and other 120V electronics). As far as I can tell, the only difference between the two 120V options is that the 6FXN4 model is TAA-compliant. 15510 Sat Aug 8 07:36:52 2020 Sanika KhadkikarConfigurationCalibration-RepairBS Seismometer - Multi-channel calibration Summary : I have been working on analyzing the seismic data obtained from the 3 seismometers present in the lab. I noticed while looking at the combined time series and the gain plots of the 3 seismometers that there is some error in the calibration of the BS seismometer. The EX and the EY seismometers seem to be well-calibrated as opposed to the BS seismometer. The calibration factors have been determined to be : BS-X Channel: $\dpi{150} \small {\color{Blue} 2.030 \pm 0.079 }$ BS-Y Channel: $\dpi{150} \small {\color{Blue} 2.840 \pm 0.177 }$ BS-Z Channel: $\dpi{150} \small {\color{Blue} 1.397 \pm 0.182 }$ Details : The seismometers each have 3 channels i.e X, Y, and Z for measuring the displacements in all the 3 directions. The X channels of the three seismometers should more or less be coherent in the absence of any seismic excitation with the gain amongst all the similar channels being 1. So is the case with the Y and Z channels. After analyzing multiple datasets, it was observed that the values of all the three channels of the BS seismometer differed very significantly from their corresponding channels in the EX and the EY seismometers and they were not calibrated in the region that they were found to be coherent as well. Method : Note: All the frequency domain plots that have been calculated are for a sampling rate of 32 Hz. The plots were found to be extremely coherent in a certain frequency range i.e ~0.1 Hz to 2 Hz so this frequency range is used to understand the relative calibration errors. The spread around the function is because of the error caused by coherence values differing from unity and the averages performed for the Welch function. 9 averages have been performed for the following analysis keeping in mind the needed frequency resolution(~0.01Hz) and the accuracy of the power calculated at every frequency. 1. I first analyzed the regions in which the similar channels were found to be coherent to have a proper gain analysis. The EY seismometer was found to be the most stable one so it has been used as a reference. I saw the coherence between similar channels of the 2 seismometers and the bode plots together. A transfer function estimator was used to analyze the relative calibration in between all 3 pairs of seismometers. In the given frequency range EX and EY have a gain of 1 so their relative calibration is proper. The relative calibration in between the BS and the EY seismometers is not proper as the resultant gain is not 1. The attached plots show the discrepancies clearly : • BS-X & EY-X Transfer Function : Attachment #1 • BS-Y & EY-Y Transfer Function : Attachment #2 The gain in the given frequency range is ~3. The phase plotting also shows a 180-degree phase as opposed to 0 so a negative sign would also be required in the calibration factor. Thus the calibration factor for the Y channel of the BS seismometer should be around ~3. • BS-Z & EY-Z Transfer Function : Attachment #3 The mean value of the gain in the given frequency range is the desired calibration factor and the error would be the mean of the error for the gain dataset chosen which is caused due to factors mentioned above. Note: The standard error envelope plotted in the attached graphs is calculated as follows : 1. Divide the data into n segments according to the resolution wanted for the Welch averaging to be performed later. 2. Calculate PSD for every segment (no averaging). 3. Calculate the standard error for every value in the data segment by looking at distribution formed by the n number values we obtain by taking that respective value from every segment. Discussions : The BS seismometer is a different model than the EX and the EY seismometers which might be a major cause as to why we need special calibration for the BS seismometer while EX and EY are fine. The sign flip in the BS-Y seismometer may cause a lot of errors in future data acquisitions. The time series plots in Attachment #4 shows an evident DC offset present in the data. All of the information mentioned above indicates that there is some electrical or mechanical defect present in the seismometer and may require a reset. Kindly let me know if and when the seismometer is reset so that I can calibrate it again. 15526 Fri Aug 14 10:10:56 2020 JonConfigurationVACVacuum repairs today The vac system is going down now for planned repairs [ELOG 15499]. It will likely take most of the day. Will advise when it's back up. 15527 Sat Aug 15 02:02:13 2020 JonConfigurationVACVacuum repairs today Vacuum work is completed. The TP2 and TP3 interlocks have been overhauled as proposed in ELOG 15499 and seem to be performing reliably. We're now back in the nominal system state, with TP2 again backing for TP1 and TP3 pumping the annuli. I'll post the full implementation details in the morning. I did not get to setting up the new UPS units. That will have to be scheduled for another day.  Quote: The vac system is going down now for planned repairs [ELOG 15499]. It will likely take most of the day. Will advise when it's back up. 15528 Sat Aug 15 15:12:22 2020 JonConfigurationVACOverhaul of small turbo pump interlocks # Summary Yesterday I completed the switchover of small turbo pump interlocks as proposed in ELOG 15499. This overhaul altogether eliminates the dependency on RS232 readbacks, which had become unreliable (glitchy) in both controllers. In their place, the V4(5) valve-close interlocks are now predicated on an analog controller output whose voltage goes high when the rotation speed is >= 80% of the nominal setpoint. The critical speed is 52.8 krpm for TP2 and 40 krpm for TP3. There already exist hardware interlocks of V4(5) using the same signals, which I have also tested. # Interlock signal Unlike the TP1 controller, which exposes simple relays whose open/closed states are sensed by Acromags, what the TP2(3) controllers output is an energized 24V signal for controlling such a relay (output circuit pictured below). I hadn't appreciated this difference and it cost me time yesterday. The ultimate solution was to route the signals through a set of new 24V Phoenix Contact relays installed inside the Acromag chassis. However, this required removing the chassis from the rack and bringing it to the electronics bench (rather than doing the work in situ, as I had planned). The relays are mounted to the second DIN rail opposite the Acromags. Each TP2(3) signal controls the state of a relay, which in turn is sensed using an Acromag XT1111. # Signal routing The TP2(3) "normal-speed" signals are already in use by hardware interlocks of V4(5). Each signal is routed into the main AC relay box, where it controls an "interrupter" relay through which the Acromag control signal for the main V4(5) relay is passed. These signals are now shared with the digital controls system using a passive DB15 Y-splitter. The signal routing is shown below. # Interlock conditions The new turbo-pump-related interlock conditions and their channel predicates are listed below. The full up-to-date channel list and wiring assignments for c1vac are maintained here.  Channel Type New? Interlock-triggering condition C1:Vac-TP1_norm BI No Rotation speed < 90% nominal setpoint (29 krpm) C1:Vac-TP1_fail BI No Critical fault occurrence C1:Vac-TP1_current AI No Current draw > 4 A C1:Vac-TP2_norm BI Yes Rotation speed < 80% nominal setpoint (52.8 krpm) C1:Vac-TP3_norm BI Yes Rotation speed < 80% nominal setpoint (40 krpm) There are two new channels, both of which provide a binary indication of whether the pump speed is outside its nominal range. I did not have enough 24V relays to also add the C1:Vac-TP2(3)_fail channels listed in ELOG 15499. However, these signals are redundant with the existing interlocks, and the existing serial "Status" readback will already print failure messages to the MEDM screens. All of the TP2(3) serial readback channels remain, which monitor voltage, current, operational status, and temperature. The pump on/off and low-speed mode on/off controls remain implemented with serial signals as well. The new analog readbacks have been added to the MEDM controls screens, circled below: # Other incidental repairs • I replaced the (dead) LED monitor at the vac controls console. In the process of finding a replacement, I came across another dead spare monitor as well. Both have been labeled "DEAD" and moved to Jordan's desk for disposal. • I found the current TP3 Varian V70D controller to be just as glitchy in the analog outputs as well. That likely indicates there is a problem with the microprocessor itself, not just the serial communications card as I thought might be the case. I replaced the controller with the spare unit which was mounted right next to it in the rack [ELOG 13143]. The new unit has not glitched since the time I installed it around 10 pm last night. 15738 Fri Dec 18 22:59:12 2020 JonConfigurationCDSUpdated CDS upgrade plan Attached is the layout for the "intermediate" CDS upgrade option, as was discussed on Wednesday. Under this plan: • Existing FEs stay where they are (they are not moved to a single rack) • Dolphin IPC remains PCIe Gen 1 • RFM network is entirely replaced with Dolphin IPC Please send me any omissions or corrections to the layout. 15742 Mon Dec 21 09:28:50 2020 JamieConfigurationCDSUpdated CDS upgrade plan  Quote: Attached is the layout for the "intermediate" CDS upgrade option, as was discussed on Wednesday. Under this plan: Existing FEs stay where they are (they are not moved to a single rack) Dolphin IPC remains PCIe Gen 1 RFM network is entirely replaced with Dolphin IPC Please send me any omissions or corrections to the layout. I just want to point out that if you move all the FEs to the same rack they can all be connected to the Dolphin switch via copper, and you would only have to string a single fiber to every IO rack, rather than the multiple now (for network, dolphin, timing, etc.). 15746 Wed Dec 23 23:06:45 2020 gautamConfigurationCDSUpdated CDS upgrade plan 1. The diagram should clearly show the host machines and the expansion chassis and the interconnects between them. 2. We no longer have any Gentoo bootserver or diskless FEs. 3. The "c1lsc" host is in 1X4 not 1Y3. 4. The connection between c1lsc and Dolphin switch is copper not fiber. I don't know how many Gbps it is. But if the switch is 10 Gbps, are they really selling interface cables that have lower speed? The datasheet says 10 Gbps. 5. The control room workstations - Debian10 (rossa) is the way forward I believe. it is true pianosa remains SL7 (and we should continue to keep it so until all other machines have been upgraded and tested on Debian 10). 6. There is no "IOO/OAF". The host is called "c1ioo". 7. The interconnect between Dolphin switch and c1ioo host is via fiber not copper. 8. It'd be good to have an accurate diagram of the current situation as well (with the RFM network). 9. I'm not sure if the 1Y1 rack can accommodate 2 FEs and 2 expansion chassis. Maybe if we clear everything else there out... 10. There are 2 "2GB/s" Copper traces. I think the legend should make clear what's going on - i.e. which cables are ethernet (Cat 6? Cat 5? What's the speed limitation? The cable? Or the switch?), which are PCIe cables etc etc. I don't have omnigraffle - what about uploading the source doc in a format that the excellent (and free) draw.io can handle? I think we can do a much better job of making this diagram reflect reality. There should also be a corresponding diagram for the Acromag system (but that doesn't have to be tied to this task). Megatron (scripts machine) and nodus should be added to that diagram as well.  Please send me any omissions or corrections to the layout. 15771 Tue Jan 19 14:05:25 2021 JonConfigurationCDSUpdated CDS upgrade plan I've produced updated diagrams of the CDS layout, taking the comments in 15476 into account. I've also converted the 40m's diagrams from Omnigraffle ($150/license) to the free, cloud-based platform draw.io. I had never heard of draw.io, but I found that it has most all the same functionality. It also integrates nicely with Google Drive.

Attachment 1: The planned CDS upgrade (2 new FEs, fully replace RFM network with Gen 1 Dolphin IPC)
Attachment 2: The current 40m CDS topology

The most up-to-date diagrams are hosted at the following links:

Please send me any further corrections or omissions. Anyone logged in with LIGO.ORG credentials can also directly edit the diagrams.

15772   Tue Jan 19 15:43:24 2021 gautamConfigurationCDSUpdated CDS upgrade plan

Not sure if 1Y1 can accommodate both c1sus2 and c1bhd as well as the various electronics chassis that will have to be installed. There may need to be some distribution between 1Y1 and 1Y3. Does Koji's new wiring also specify which racks hold which chassis?

Some minor improvements to the diagram:

1. The GPS receiver in 1X7 should be added. All the timing in the lab is synced to the 1pps from this.
2. We should add hyperlinks to the various parts datasheets (e.g. Dolphin switch, RFM switch, etc etc) so that the diagram will be truly informative and self-contained.
3. Megatron and nodus, but especially chiara (NFS server), should be added to the diagram.
15921   Mon Mar 15 20:40:01 2021 ranaConfigurationComputersinstalled QTgrace on donatella for dataviewer

I installed QTgrace using yum on donatella. Both Grace and XMgrace are broken due to some boring fight between the Fedora package maintainers and the (non existent) Grace support team. So I have symlinked it:

controls@donatella|bin> sudo mv xmgrace xmgrace_bak
controls@donatella|bin> sudo ln -s qtgrace xmgrace
controls@donatella|bin> pwd
/usr/bin

I checked that dataviewer works now for realtime and playback. Although the middle click paste on the mouse doesn't work yet.

15928   Wed Mar 17 09:05:01 2021 Paco, AnchalConfigurationComputers40m Control Room Changes
• Switched positions of allegra and donatella.
• While doing so, the hdmi cable previously used by donatella snapped. We replaced this cable by another unused cable we found connected only on one end to rossa. We should get more HDMI cables if that cable was in use for some other purpose.
• Paco bought a bluetooth speaker/mic that is placed infront of allegra and it's usb adapter is connected to iMac's keyboard in the bottom. With the new camera installed, the 40m video call environment is now complete.
• Again, we have placed allegra's monitor for place holder but it is not working and we need new monitors for it in future whenever it is going to be used.
16027   Wed Apr 14 13:16:20 2021 AnchalConfigurationComputers40m Control Room Changes
• I have confirmed that the old two monitors' backlighting is not working. One can see the impression of the display without any brightness on them. Both old monitors are on the shelf behind.
• Today we got a monitor and mouse from Mike. I had to change /etc/default/grub GRUB_GFXMODE to 1920x1200@30 on allegra for it to work with the(any) monitor.
• Allegra is Debian 10 with latest cds-workstation installed on it. It is a good test station to migrate our existing scripts to start using updated cds-workstation configuration.
 Quote: Again, we have placed allegra's monitor for place holder but it is not working and we need new monitors for it in future whenever it is going to be used.

16163   Wed May 26 11:45:57 2021 Anchal, PacoConfigurationIMCMC2 analog camera

[Anchal, Paco]

We went near the MC2 area and opened the lid to inspect the GigE and analog video monitors for MC2. Looked like whatever image is coming through the viewport is split into the GigE (for beam tracking) and the analog monitor. We hooked the monitor found on the floor nearby and tweaked the analog video camera around to get a feel for how the "ghost" image of the transmission moves around. It looks like in order to try and remove this "extra spots" we would need to tweak the beam tracking BS. We will consult the beam tracking authorities and return to this.

16302   Thu Aug 26 10:30:14 2021 JamieConfigurationCDSfront end time synchronization fixed?

I've been looking at why the front end NTP time synchronization did not seem to be working.  I think it might not have been working because the NTP server the front ends were point to, fb1, was not actually responding to synchronization requests.

I cleaned up some things on fb1 and the front ends, which I think unstuck things.

On fb1:

• stopped/disabled the default client (systemd-timesyncd), and properly installed the full NTP server (ntp)
• the ntp server package for debian jessie is old-style sysVinit, not systemd.  In order to make it more integrated I copied the auto-generated service file to /etc/systemd/system/ntp.service, and added and "[install]" section that specifies that it should be available during the default "multi-user.target".
• "enabled" the new service to auto-start at boot ("sudo systemctl enable ntp.service")
• made sure ntp was configured to serve the front end network ('broadcast 192.168.123.255') and then restarted the server ("sudo systemctl restart ntp.service")

For the front ends:

• on fb1 I chroot'd into the front-end diskless root (/diskless/root) and manually specifed that systemd-timesyncd should start on boot by creating a symlink to the timesyncd service in the multi-user.target directory:
$sudo chroot /diskless/root$ cd /etc/systemd/system/multi-user.target.wants
$ln -s /lib/systemd/system/systemd-timesyncd.service • on the front end itself (c1iscex as a test) I did a "systemctl daemon-reload" to force it to reload the systemd config, and then restarted the client ("systemctl restart systemd-timesyncd") • checked the NTP synchronization with timedatectl: controls@c1iscex:~ 0$ timedatectl
Local time: Thu 2021-08-26 11:35:10 PDT
Universal time: Thu 2021-08-26 18:35:10 UTC
RTC time: Thu 2021-08-26 18:35:10
Time zone: America/Los_Angeles (PDT, -0700)
NTP enabled: yes
NTP synchronized: yes
RTC in local TZ: no
DST active: yes
Last DST change: DST began at
Sun 2021-03-14 01:59:59 PST
Sun 2021-03-14 03:00:00 PDT
Next DST change: DST ends (the clock jumps one hour backwards) at
Sun 2021-11-07 01:59:59 PDT
Sun 2021-11-07 01:00:00 PST
controls@c1iscex:~ 0$ Note that it is now reporting "NTP enabled: yes" (the service is enabled to start at boot) and "NTP synchronized: yes" (synchronization is happening), neither of which it was reporting previously. I also note that the systemd-timesyncd client service is now loaded and enabled, is no longer reporting that it is in an "Idle" state and is in fact reporting that it synchronized to the proper server, and it is logging updates: controls@c1iscex:~ 0$ sudo systemctl status systemd-timesyncd
â— systemd-timesyncd.service - Network Time Synchronization
Loaded: loaded (/lib/systemd/system/systemd-timesyncd.service; enabled)
Active: active (running) since Thu 2021-08-26 10:20:11 PDT; 1h 22min ago
Docs: man:systemd-timesyncd.service(8)
Main PID: 2918 (systemd-timesyn)
Status: "Using Time Server 192.168.113.201:123 (ntpserver)."
CGroup: /system.slice/systemd-timesyncd.service
â””â”€2918 /lib/systemd/systemd-timesyncd

Aug 26 10:20:11 c1iscex systemd[1]: Started Network Time Synchronization.
Aug 26 10:20:11 c1iscex systemd-timesyncd[2918]: Using NTP server 192.168.113.201:123 (ntpserver).
Aug 26 10:20:11 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 64s/+0.000s/0.000s/0.000s/+26ppm
Aug 26 10:21:15 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 128s/-0.000s/0.000s/0.000s/+25ppm
Aug 26 10:23:23 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 256s/+0.001s/0.000s/0.000s/+26ppm
Aug 26 10:27:40 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 512s/+0.003s/0.000s/0.001s/+29ppm
Aug 26 10:36:12 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 1024s/+0.008s/0.000s/0.003s/+33ppm
Aug 26 10:53:16 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 2048s/-0.026s/0.000s/0.010s/+27ppm
Aug 26 11:27:24 c1iscex systemd-timesyncd[2918]: interval/delta/delay/jitter/drift 2048s/+0.009s/0.000s/0.011s/+29ppm
controls@c1iscex:~ 0\$

So I think this means everything is working.

I then went ahead and reloaded and restarted the timesyncd services on the rest of the front ends.

We still need to confirm that everything comes up properly the next time we have an opportunity to reboot fb1 and the front ends (or the opportunity is forced upon us).

There was speculation that the NTP clients on the front ends (systemd-timesyncd) would not work on a read-only filesystem, but this doesn't seem to be true.  You can't trust everything you read on the internet.

50   Thu Nov 1 19:53:02 2007 Andrey RodionovBureaucracyPhotosTobin's picture
51   Thu Nov 1 19:53:34 2007 Andrey RodionovBureaucracyPhotosRobert's photo
52   Thu Nov 1 19:54:22 2007 Andrey RodionovBureaucracyPhotosRana's photo
53   Thu Nov 1 19:55:03 2007 Andrey RodionovBureaucracyPhotosAndrey's photo
54   Thu Nov 1 19:55:59 2007 Andrey RodionovBureaucracyPhotosAndrey, Tobin, Robert - photo
55   Thu Nov 1 19:58:07 2007 Andrey RodionovBureaucracyPhotosSteve and Tobin's picture
57   Fri Nov 2 08:59:30 2007 steveBureaucracySAFETYthe laser is ON
The psl laser is back on !
75   Wed Nov 7 02:14:08 2007 AndreyBureaucracyIOOMore information about MC2 ringdown
As Tobin wrote two hours ago, we (Andrey, Tobin, Robert) made a series of ringdown measurements for MC2
in the spirit of the measurement described by Rana -> see
entry from Mon Oct 29 23:47:29 2007, rana, Other, IOO, MC Ringdowns.

I attach here some pictures that we saw on the screen of the scope, but I need to admit that I am not experienced enough to present a nice fit to these data, although I attach fits that I am able to do today.

I definitely learned a lot of new Matlab functions from Tobin - thanks to him!, but I need to learn two more things:

Firstly, I do not know how to delete "flat" region (regions before the ringdown starts) in Matlab ->
I needed to delete the entries for times before the ringdown ("negative times") by hand in the text-file, which is extremely non-elegant method;

Secondly, I tried to approximate the ringdown curve by a function ydata=a*exp(b*xdata) but I am not exactly sure if this equation of the fitting curve is a good fit or if a better equation can be used.

It seems, in this situation it is better for me to ask more experienced "comrades" on November 7th.

P.S. It seems I really like the type of message "Bureaucracy" - I put it for every message. As Alain noted, maybe that is because some things are very bureacratized in the former USSR / Russia. By the way, when I was young, November 7th was one of two most important holidays in the USSR - I liked that holiday because I really liked military parades on the red square. I attach a couple of pictures. November 7 is the anniversary of the Revolution of 1917.
113   Fri Nov 16 18:46:49 2007 steveBureaucracyPSL MOPA was turned off & on
The "Mohana" boys scouts and their parents visited the 40m lab today.
The laser was turned off for their safety.
It is back on !
115   Mon Nov 19 14:32:10 2007 steveBureaucracySAFETYgrad student safety training
John Miller and Alberto Stochino has received the 40m safety bible.
They still have to read the laser operation manual and sign off on it.
130   Wed Nov 28 12:43:53 2007 AndreyBureaucracy Here was the PDF-file of my presentation

I was making a report with powerpoint presentation during that Wednesday's 40-m meeting.

Here was the pdf-file, but LATER IN THE EVENING I CREATED A WIKI-40M-page describing the algorithm, and now the pdf-file is ON THAT WIKI-40M PAGE.

NOTE ADDED AFTER THE PRESENTATION: I double checked, I am indeed taking the root-mean-square of a difference, as we discussed during my talk.

My slide #17 "Calculation of differential length" was wrong, but now I corrected it.
135   Wed Nov 28 19:02:41 2007 AndreyBureaucracyWIKI-40M UpdateNew WIKI-40M page describing Matlab Suspension Modeling

I created the WIKI-40m page with some details about my today's talk on the 40-m lab meeting.

The address is:

http://lhocds.ligo-wa.caltech.edu:8000/40m/Modeling_of_suspensions

(or you can go to the main page, http://lhocds.ligo-wa.caltech.edu:8000/40m/ , and click on the link "Modeling of suspensions").

The WIKI-40m page describes my transfer functions and contains the pdf-file of my presentation.
224   Thu Jan 3 12:38:49 2008 robBureaucracyTMISore throat

 Quote: I did not feel anything wrong yesterday, but unfortunately I have a very much sore throat today. I need to drink warm milk with honey and rinse my throat often today. So far I do not have other illness symptomes (no fever), so I hope that this small disease will not last for a long time, but I feel that it is better for me to cure my sore throat today at home (and probably it is safer for others in 40-m). I took yesterday the book "Digital Signal Processing", so I have it for reading at home. Hope to see you tomorrow.

I've added a new category--TMI--for entries along these lines.
262   Thu Jan 24 22:52:18 2008 AndreyBureaucracyGeneralAnts around a dirty glass (David - please read!)

Dear coleagues,

there are rains outside these days, so ants tend to go inside our premises.

David was drinking some beverage from a glass earlier today (at 2PM) and left a dirty glass near the computer.

There are dozens, if not hundreds, of ants inside of that glass now.

Of course, I am washing this glass.

A.
279   Mon Jan 28 12:42:48 2008 DmassBureaucracyTMICoffee
There is tea in the coffee carafe @ the 40m. It is sitting as though it were fresh coffee. There is also nothing on the post it.
339   Fri Feb 22 21:19:38 2008 AndreyBureaucracyComputer Scripts / ProgramsMDV library does not work at "LINUX 2"

While working on Thursday evening with Matlab scripts "dttfft2" and "get_data", I noticed that mDV library does not work at computer "LINUX 2" (the third computer in the control-room if you enter it from the restroom). There are multiple error messages if we try to run "hello_world", "dttfft2" or "get_data". In order to take data from accelerometers, I changed the computer - I was working from "LINUX 3" computer, the most right computer in the control room, but for the future someone should resolve the issue at "LINUX 2". I am not experienced enough to revive the correct work of mDV directory at "LINUX 2".

Andrey.
343   Thu Feb 28 12:31:33 2008 robBureaucracyComputer Scripts / ProgramsMDV library does not work at "LINUX 2"

 Quote: While working on Thursday evening with Matlab scripts "dttfft2" and "get_data", I noticed that mDV library does not work at computer "LINUX 2" (the third computer in the control-room if you enter it from the restroom). There are multiple error messages if we try to run "hello_world", "dttfft2" or "get_data". In order to take data from accelerometers, I changed the computer - I was working from "LINUX 3" computer, the most right computer in the control room, but for the future someone should resolve the issue at "LINUX 2". I am not experienced enough to revive the correct work of mDV directory at "LINUX 2". Andrey.

This turned out to be due to /frames not being mounted on linux2, as a result of a reboot. The issue is discussed in entry 270. I remounted the /frames, and added a line to mdv_config.m to check whether the frames are mounted.
382   Fri Mar 14 16:56:03 2008 DmassBureaucracyComputersNew 40m control machine.
I priced out a new control machine from Dell and had Steve buy it.

GigE cards (jumbo packet capable) will be coming seperately.

Specs:
Quad core (2+GHz)
4 Gigs @ 800MHz RAM
24" LCD
low end video card (Nvidia 8300 - analog + digital output for dual head config)

No floppy drive on this one (yet?)
488   Tue May 20 09:28:42 2008 steveBureaucracySAFETYsafety traning for 40m
Tara Chalernsongsak, new gradstudent for K. Libbrecht was introduced to the basics of the 40m operations.
491   Thu May 22 11:21:45 2008 steveBureaucracySAFETYearly surf sudent
Caltech under grad Eric Mintun received the 40m safety training.
Now he has to read and sign SOP of laser and ifo.
He'll be working with GigE cameras with Joe
505   Thu May 29 16:49:49 2008 steveBureaucracyPhotosYoichi has arrived
Yoichi had his first 40m meeting. We welcomed him and Tobin, who is visiting, by sugar napoleons that
Bob made.
511   Mon Jun 2 12:20:35 2008 josephbBureaucracyCamerasBeam scan has moved
The beamscan has been moved from the Rana lab back over to the 40m, to be used to calibrate the Prosilica cameras.
523   Fri Jun 6 15:56:00 2008 steveBureaucracySAFETYYoichi received safety training
Yoichi Aso received 40m specific safety training.
552   Mon Jun 23 15:22:04 2008 ranaBureaucracySAFETYLaser Safety Walkthrough today
ELOG V3.1.3-

format: plain


text:
##### Notes

This printable supports Common Core Mathematics Standard 6.G.A.1

##### Print Instructions

NOTE: Only your test content will print.
To preview this test, click on the File menu and select Print Preview.

See our guide on How To Change Browser Print Settings to customize headers and footers before printing.

# Areas of Polygons (Grade 6)

Print Test (Only the test content will print)

## Areas of Polygons

1.
Which of the following describes a correct method of finding the area of a trapezoid?
1. Compose a right triangle, find its area, then divide the area by 2.
2. Compose a parallelogram, find its area, then divide the area by 2.
3. Decompose into 2 right triangles, find the area of 1 triangle, then multiply the area by 2.
4. Decompose into 2 parallelograms, find the area of 1 parallelogram, then multiply the area by 2.
2.
Calculate the area of the trapezoid if $bar(AD)$ measures 10 cm, $bar(BC)$ measures 8 cm and the height is 5 cm.
1. $40 cm^2$
2. $45 cm^2$
3. $50 cm^2$
4. $90 cm^2$
3.
What is the area of a triangle with a base of 16 inches and a height of 12 inches?
1. 96 square inches
2. 48 square inches
3. 36 square inches
4. 86 square inches
4.
$bar (BC)$ measures 12 m and $bar (AB)$ measures 4 m.
What is the area of right triangle ABD?
1. $16 m^2$
2. $24 m^2$
3. $32 m^2$
4. $48 m^2$
5.
The length of $bar (AD$ is 12 units and the height of the parallelogram is 6 units. What is the area of triangle BCD?
1. $18 units^2$
2. $30 units^2$
3. $36 units^2$
4. $72 units^2$
6.
Triangles ABF and ECD are congruent. If triangle ECD has an area of 15 square cm and trapezoid ABCD has an area of 80 square cm, what is the area of trapezoid FBCE?
1. 30 square cm
2. 50 square cm
3. 65 square cm
4. 90 square cm
7.
Use the following information to find the area of pentagon ABCDE.

$bar(BD) = 8 cm$
$bar(AE) = 6 cm$

The height of triangle BCD is 3 cm
The height of trapezoid ABDE is 5 cm
1. $12 cm^2$
2. $22 cm^2$
3. $35 cm^2$
4. $47 cm^2$
8.
The area of square ABCD is 64 square units. What is the area of triangle ACD?
1. 16 square units
2. 24 square units
3. 32 square units
4. 40 square units
9.
Find the area of triangle where the base is 6 in and height is 5 in.

10.
The height of parallelogram ABED is 7 inches. $bar(AC$ is 3 inches and $bar(AD$ is 12 inches. What is the area of parallelogram BCDF?

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text:
# How do you solve  sqrt[x+2]=sqrt[4-x] and find any extraneous solutions?

Oct 10, 2017

$x = 1$

#### Explanation:

$\text{to access the contents of the radicals}$

$\textcolor{b l u e}{\text{square both sides}}$

•color(white)(x)sqrtaxxsqrta=(sqrta)^2=a

${\left(\sqrt{x + 2}\right)}^{2} = {\left(\sqrt{4 - x}\right)}^{2}$

$\Rightarrow x + 2 = 4 - x$

$\text{add x to both sides}$

$x + x + 2 = 4 \cancel{- x} \cancel{+ x}$

$\Rightarrow 2 x + 2 = 4$

$\text{subtract 2 from both sides}$

$2 x \cancel{+ 2} \cancel{- 2} = 4 - 2$

$\Rightarrow 2 x = 2$

$\text{divide both sides by 2}$

$\frac{\cancel{2} x}{\cancel{2}} = \frac{2}{2}$

$\Rightarrow x = 1$

$\textcolor{b l u e}{\text{As a check}}$

Substitute this value into the equation and if both sides are equal then it is the solution.

$\text{left side } = \sqrt{1 + 2} = \sqrt{3}$

$\text{right side } = \sqrt{4 - 1} = \sqrt{3}$

$\Rightarrow x = 1 \text{ is the solution}$

There are no other solutions hence no extraneous solutions.


text:
# IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity

Oncotarget. 2016; 7:47864-47874. https://doi.org/10.18632/oncotarget.10012

Metrics: PDF 1415 views  |   HTML 2262 views  |   ?

## Abstract

Liang Cheng1,*, Hongbo Shi1,*, Zhenzhen Wang1,*, Yang Hu2, Haixiu Yang1, Chen Zhou1, Jie Sun1, Meng Zhou1

1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China

2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China

*These authors have contributed equally to this work

Correspondence to:

Meng Zhou, email: [email protected]

Jie Sun, email: [email protected]

Keywords: long non-coding RNAs, lncRNA functional similarity, integrated network, lncRNA-disease associations

Received: March 03, 2016    Accepted: May 23, 2016    Published: June 14, 2016

ABSTRACT

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim.

## INTRODUCTION

Recent large-scale genomic and transcriptomic analysis has shown that only less than 2% of genome sequence can encode protein, and functional non-coding transcripts constitute a large portion of the genome transcripts [1, 2]. Long non-coding RNAs (lncRNAs), a recently discovered class of non-coding RNAs, was arbitrarily defined as mRNA-like transcripts longer than 200 nucleotides that have no or little protein-coding capacity [3].

The accumulating evidence suggested that lncRNAs are a novel and crucial layer of gene regulation network, and play important roles in various biological processes, such as imprinting, developmental regulation, chromatin modification, transcriptional regulation, dosage compensation and so on [37]. The dysregulated lncRNA expression has also been observed and implicated in the development and progression of complex diseases [820]. Although tens of thousands of lncRNAs have been discovered and recorded in several public databases, such as GENCODE [21], NONCODE [22], LNCipedia [23], only a handful of lncRNAs were well-studied and characterized functionally. For example, only 182 functional lncRNAs were manually curated from existing literature in lncRNAdb [24].

It has shown to be an efficient way to infer potential function for novel genes by studying the functional similarity between genes with known functions or associated with specific diseases and that with unknown functions. Many methods have been developed to measure the functional similarity between protein-coding genes or miRNAs which accelerated functional analysis of protein-coding genes and miRNAs [2528]. In consideration of the large number and limited knowledge of lncRNAs, it is urgent to develop novel methods to measure lncRNA functional similarity (LFS) for inferring lncRNA function and mining the associations between lncRNAs and diseases. Several efforts have been made to meet the urgent need in recent studies. For example, Sun and colleagues firstly introduced semantic similarity between lncRNAs-related diseases to calculate LFS (SemLncSim) which was used to predict disease-related lncRNAs [29]. SemLncSim was further improved by Chen et al. through considering lncRNA-disease associations and semantic similarity between diseases [30]. Another method, LFSCM, was proposed by Chen et al. to calculate LFS based on the lncRNA-related miRNA information [31].

Improved knowledge has suggested that lncRNAs were involved in diverse biological processes by negatively or positively regulating gene expression at both the post-transcriptional and transcriptional level [32]. For example, lncRNAs can function as key competing endogenous RNAs (ceRNAs) to communicate with mRNAs and regulate with each other by competing with common miRNAs at the post-transcriptional level [33, 34]. LncRNA also could negatively or positively regulate protein-coding gene expression in cis or trans at the transcriptional level. Thus, a more accurate measurement should take fully into account both lncRNA-related miRNAs/mRNAs and the functional communication among them. In this study, we developed an integrative framework, called IntNetLncSim, to infer human LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. IntNetLncSim is freely accessible at (http://www.bio-bigdata.com/IntNetLncSim).

## RESULTS

### Performance evaluation of IntNetLncSim

As mentioned above, lncRNA performed their function by negatively or positively regulating gene expression at both the post-transcriptional and transcriptional level. Therefore, it is expected that functionally related lncRNAs are often associated with functionally similar mRNAs or miRNAs. Therefore, we assessed relationships between IntNetLncSim functional similarity of lncRNAs and the similarity of the lncRNA-related mRNA sets (LmRSets) or miRNA sets (LmiRSets). In this study, functional similarity between mRNA sets was calculated by GsNetCom [35], which is a web-based toolkit to measure the functional association between two gene sets. In addition, functional similarity between miRNA sets was measured using Sun’s method [25]. As a result, IntNetLncSim functional similarity of lncRNAs was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424, p=2.2e-16; Figure 1A) and LmiRSet (Pearson correlation γ2=0.2601, p=2.2e-16; Figure 1C). We further grouped lncRNA pairs into different groups according to LFS by a step of 0.1 and calculated the average LFS and the similarity of the LmRSet and LmiRSet. Then, the same correlation analysis was performed. As shown in Figure 1B and 1C, positive correlation between lncRNA functional similarity by our method and functional similarity of the LmRSet (Pearson correlation γ2=0.9753, p=3.299e-07; Figure 1B) and LmiRSet (Pearson correlation γ2=0.9448, p =1.181e-05; Figure 1D) was observed. Taken together, these results suggested that IntNetLncSim can reflect the correlations between LFS and that of LmRSet or LmiRSet.

Figure 1: Performance evaluation of IntNetLncSim. A. The distribution of the similarity of the LmRSet. A solid circle denotes the functional similarity of a pair of lncRNAs in the horizontal axis and the similarity of the LmRSet in the vertical axis. The dashed line is the linear regression line generated by the least squares of the data points. B. The distribution of the similarity of the LmRSet based on the grouped lncRNA pairs. C. The distribution of the similarity of the LmiRSet. D. The distribution of the similarity of the LmiRSet based on the grouped lncRNA pairs. E. The distribution of IntNetLncSim functional similarity scores of lncRNAs based on the integrated network and random network.

To further verify the reliability of IntNetLncSim, a random network based on the topology of the integrated network was introduced. We first compared the relationships between IntNetLncSim functional similarity of lncRNAs based on the random network with the similarity of the LmRSet and LmiRSet, and then compared the LFS based on the random network with the similarity based on the integrated network. As expected, IntNetLncSim functional similarity of lncRNAs based on the random network was uncorrelated with the LmRSet (Pearson correlation γ2=8.267477e-05, p=0.717) and LmiRSet (Pearson correlation γ2=-0.0003, p=0.2117). In addition, the results in Figure 1E indicated that LFS based on the integrated network was significant difference with the similarity based on the random network (Pearson correlation γ2=0.0003, p=0.2117). The average LFS score based on the integrated network (0.3017728) was significantly higher than that based on the random network (8.540267e-07). Taken together, in comparison with random network, LFS based on the integrated network is more relevant with the similarity of the LmRSet and LmiRSet.

In order to assess the effects of mRNA and miRNAs in the integrated network, we ignored miRNA and mRNA, respectively. The correlation between LFS by ignoring miRNA and the similarity of the LmRSet is 0.7590, which is higher than that of IntNetLncSim (γ2=0.5385). However, the correlation between LFS by ignoring miRNA and the similarity of the LmiRSet (γ2=0.0467) is much lower than that of IntNetLncSim (γ2=0.2504). The correlation between LFS by ignoring mRNA and the similarity of the LmiRSet is 0.6735, which is higher than that of IntNetLncSim (γ2=0.2504). However, the correlation between LFS by ignoring mRNA and the similarity of LmRSet (γ2=0.0192) is much lower than that of IntNetLncSim (γ2=0.5385). Overall, the performance wasn’t significantly affected after ignoring mRNA or miRNA. In comparison, the performance is more stable as using the integrated network. Because lncRNAs function at both the post-transcriptional and transcriptional level, the function of lncRNA could be reflected by both miRNA and mRNA. Therefore, the performance of the integrated network is more and stable.

### Comparisons with other existing similar methods

Because LFS of diverse lncRNA sets was calculated by different methods, the performance of IntNetLncSim should be compared with the performance of SemLncSim, LNCSIM, and LFCSM, respectively. For example, to compare the performance of IntNetLncSim and SemLncSim, common lncRNAs based on these two methods were extracted first. Then, the Pearson correlation between LFS of these common lncRNAs and the similarity of the LmRSet and LmiRSet could be calculated as following:

$ρX,Y=cov(X,Y)σx⋅σy,$   (1)

where X represents LFS using IntNetLncSim or SemLncSim, Y is the similarity of the LmRSet or LmiRSet, σx and σy are the variance of X and Y, respectively, and cov(X,Y) represents covariance between X and Y. Finally, the performance of IntNetLncSim and SemLncSim can be reflected by this correlation.

SemLncSim was the first method to compute the similarity between lncRNAs. The correlations between functional similarity of lncRNAs and the similarity of the LmRSet and LmiRSet were shown in the Figure 2A. Obviously, the correlation between LFS by IntNetLncSim and the similarity of the LmRSet (γ2=0.6596, p=2.2e-16) is significantly higher than that of SemLncSim (Pearson correlation γ2=-0.0293, p=0.259). Although correlation (0.0737) seems to be improved slightly between LFS by SemLncSim and the similarity of the LmiRSet (Pearson correlation γ2=0.0737), the significant level of this correlation was also very low (p=0.1364). In comparison with SemLncSim, the correlations between LFS by IntNetLncSim and the similarity of the LmiRSet were much higher (Pearson correlation γ2=0.4064, p=2.2e-16). These results showed that LFS by IntNetLncSim is much more relevant with the similarity of the LmRSet and LmiRSet than LFS by SemLncSim.

Figure 2: The comparison of IntNetLncSim with previous similar methods. A. The correlation between LFS by IntNetLncSim and SemLncSim and the similarity of LmRSet and LmiRSet. B. The correlation between LFS by IntNetLncSim and LNCSIM and the similarity of LmRSet and LmiRSet. C. The correlation between LFS by IntNetLncSim and LFSCM and the similarity of LmRSet and LmiRSet.

LNCSIM was another method to calculate the similarity between lncRNAs which utilized the semantic similarity between diseases. LNCSIM1 and LNCSIM2 are two types of LNCSIM based on Resnik’s [36] and Wang’s method [37], respectively. After combining with IntNetLncSim, 55 common lncRNAs and 29 common lncRNAs that can regulate mRNAs and miRNAs were obtained, respectively. The correlations between functional similarity of these common lncRNAs and the similarity of the LmRSet and LmiRSet were shown in the Figure 2B. As a result, the performance of LNCSIM1 and LNCSIM2 appeared to be roughly the same. For example, the correlation between LFS by LNCSIM1 and the similarity of the LmRSet is -0.0436 (p=0.0931), and that of LNCSIM2 is -0.0467 (p=0.0722). In contrast, IntNetLncSim achieved a better performance. For example, the correlation between LFS by IntNetLncSim and the LmRSet is 0.6445 (p=2.2e-16). These results showed that the performance of IntNetLncSim is much better than LNCSIM.

LFSCM measures LFS between lncRNAs based on the miRNA information of lncRNAs. These interactions are part of the lncRNA regulatory network. Thus, lncRNAs in LFCSM are contained in IntNetLncSim. As shown in Figure 2C, the correlations between LFS by LFSCM and the similarity of the LmiRSet is 0.6330, which is higher than that of IntNetLncSim (γ2=0.2626). However, the correlations between LFS by LFSCM and the similarity of LmRSet (γ2=0.0244) is significantly lower than that of IntNetLncSim (γ2=0.5400) (Figure 2C). If only considering the correlation based on the similarity of the LmiRSet, the performances of LFSCM and IntNetLncSim were both very well. After introducing correlation based on the similarity of the LmRSet, the advantage of IntNetLncSim was obvious. These results showed that IntNetLncSim was more comprehensive and stable.

### lncRNA functional similarity network (LFSN)

We calculated similarity scores for all the pairs of lncRNAs in our integrated network by IntNetLncSim. Then, we got the z-score of these similarity scores. As a result, one-sided P-value was accessed for each similarity score. These LFS scores with P-values were used to construct LFSN (http://www.bio-bigdata.com/IntNetLncSim), which was utilized to predict novel associations between lncRNAs and diseases in the next section.

### Case studies

By applying the above constructed LFSN, novel candidate disease-related lncRNAs were predicted based on random walk with restart (RWR) algorithm (see Materials and Methods). To evaluate the performance of the LFSN, leave-one-out cross validation of 150 known experimentally confirmed lncRNA-disease associations, including 40 diseases with at least two lncRNAs, was used for this assessment. For a disease d of interest, each known lncRNA associated with disease d was left out as the testing case, and the remaining known disease d-related lncRNAs were used as seed nodes. All the lncRNAs except the known disease d-related lncRNAs were considered as candidate lncRNAs. We then examined how well the testing lncRNA ranked relative to the candidate lncRNAs. If the ranking of this testing lncRNA exceeded a given cutoff, we regarded this lncRNA-disease association as successfully predicted. As a result, an area under the ROC curve (AUC) of 0.7300 was achieved (Figure 3), which demonstrated that our constructed LFSN was effective in recovering known experimentally confirmed disease-related lncRNAs.

Figure 3: ROC curve and AUC value of our method based on leave-one-out cross validation on 150 known experimentally verified lncRNA-disease associations.

To further indicate the application of our constructed LFSN in identifying novel disease-related lncRNAs, case studies of liver cancer and breast cancer were examined. For a given disease, the known disease-related lncRNAs were served as seed lncRNAs, and all the non-seed lncRNAs were ranked based on RWR algorithm. The top 20 lncRNAs in the ranked list were investigated. We manually checked these lncRNA-disease associations in the published literature and the results were shown in Table 1. Two and three of the top 20 predicted lncRNAs were validated in liver cancer and breast cancer, respectively, and most of them had high ranks in the predicted lncRNA lists. For example, expression quantitative trait loci in ZNRD1-AS1 were recently found to affect both HBV infection and liver cancer development [38]. High expression of NEAT1 in patients with breast cancer was reported to be correlated with poor survival [39]. All these results indicated that our constructed LFSN was effective in identifying novel disease-related lncRNAs, and the LFS method we proposed was reliable.

Table 1: The novel lncRNA-disease associations confirmed by literature mining

lncRNA name

Ranking

References

Liver cancer

ZNRD1-AS1

10

[38]

ZNF718

20

[52]

Breast cancer

SNHG1

8

[53]

NEAT1

9

[39]

SEC22B

12

[54]

### System design and implementation

In order to facilitate querying lncRNA functional similarities and potential associations between lncRNAs and diseases, a web-based system was designed and implemented. The system was implemented on a JavaEE framework and run on our web server (http://www.bio-bigdata.com/IntNetLncSim). The three-layer architecture involving DATABASE, WEB INTERFACE, and VIEW layer is shown in Figure 4.

Figure 4: System overview.

## DISCUSSION

The importance of the function of non-coding RNA had been reflected in the previous research. Unfortunately, functional inferring of non-coding RNA is not easy in comparison with those of coding RNA. LncRNA is a new type of non-coding RNA that contribute to the largest number of RNAs in human, so it is urgent to develop novel methods for infering function of lncRNA. Recently, the function similarity of lncRNAs was proved that can be used to find potential function of lncRNAs [29]. In this study, we devised a new method, IntNetLncSim, for improving the performance of calculating the LFS by the integrated network. And then, the method was utilized to construct LFSN for predicting novel associations between lncRNAs and diseases. Furthermore, a web interface (http://www.bio-bigdata.com/IntNetLncSim) has been designed for accessing LFS and associations between lncRNAs and diseases.

IntNetLncSim is based on an integrated network involving lncRNA regulatory network, miRNA-mRNA interaction network, and mRNA-mRNA interaction network. In comparison with several previous methods, the integrated network covered much more lncRNAs (Table 2). Moreover, the performance of IntNetLncSim was proven to be very reliable and stable in the correlation with the similarity of the LmRSet and LmiRSet.

Table 2: The number of lncRNAs in SemLncSim, LNCSIM, LFCSM and IntNetLncSim, respectively

Method

The number of lncRNAs

Data Source

SemLncSim

129

LNCSIM

104

(LNCSIM1, LNCSIM2)

LFCSM

1114

starBase

IntNetLncSim

6314

starBase

LFSN was constructed based on the functional similarity between lncRNAs by IntNetLncSim. The performance of LFSN was proven to be reliable for recovering experimentally verified lncRNA-disease associations from LncRNADisease by leave-one-out cross validation. Then, the LFSN was applied to predict novel lncRNA-disease associations not in LncRNADisease. Five predicted associations between lncRNAs and two kinds of important cancer (liver cancer and breast cancer) were validated from the latest researches. This means that the LFSN could be exploited to predict novel relationships between lncRNAs and diseases.

It should be noted that IntNetLncSim relied on our integrated network. According to Figure 1E, the result of random work could be affected by a large amount of missing interactions among mRNAs, miRNAs, and lncRNAs. Therefore, the performance of IntNetLncSim may be improved by the exposal of newly interactions among mRNAs, miRNAs, and lncRNAs.

## MATERIALS AND METHODS

### Data source

#### Human mRNA-lncRNA and miRNA-lncRNA interaction data sets

The mRNA-lncRNA interaction and miRNA-lncRNA interaction data sets were downloaded from starBase v2.0 database [40] in October 2015, which provided experimentally confirmed mRNA-lncRNA and miRNA-lncRNA interactions based on large scale CLIP-Seq data. Currently, a total of 17,609 mRNA-lncRNA interactions between 33 mRNAs and 6,238 lncRNAs and 10,212 interactions between 277 miRNAs and 1,127 lncRNAs were included in this study. These miRNA-lncRNA interaction and miRNA-lncRNA interaction data sets were integrated to form a lncRNA regulatory network.

#### Human mRNA-mRNA interaction data

The mRNA-mRNA interaction dataset was downloaded from Human Protein Reference Database (HPRD) [41]. The HPRD is a resource for experimentally derived information about the human protein–protein interactions, and proteins in HPRD were mapped to mRNAs. After getting rid of duplicate interactions, 39,239 interactions between 9,616 mRNAs were obtained and formed an mRNA-mRNA interaction network.

#### Human miRNA-mRNA interaction data

The miRNA-mRNA interaction dataset was retrieved from three widely used and experimentally confirmed miRNA-target databases: TarBase (version 6.0) [42], miRTarBase (version 4.5) [43] and miRecords (version 4) [44]. These three databases were merged and the name of mature miRNAs were unified using miRBase (Release 21) [45]. Finally, 37,832 targeting pairs involving 558 miRNAs and 12,370 target genes were obtained to form a miRNA-mRNA interaction network.

#### Human lncRNA-disease association data

The human lncRNA-disease association data was incorporated into the LFSN to predict disease-related lncRNA. These associations were accessed from LncRNADisease [46], which is a resource that curated the experimentally supported disease-lncRNA association data. After discarding disease terminologies not in Disease Ontology (DO) [47] and getting rid of duplicate associations, 189 associations between 79 diseases and 60 lncRNAs were obtained.

### Methods

#### Method for calculating lncRNA functional similarity

In this study, we presented an integrative framework, IntNetLncSim, to measure the functional similarity of lncRNAs by modelling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. A schematic representation of the IntNetLncSim method is shown in Figure 5. Initially, lnc1 and lnc2 are two lncRNAs. First, an integrative network was constructed based on lncRNA-regulatory network, mRNA-mRNA interaction network, and miRNA-mRNA interaction network. Then, ITM Probe [48] was applied for assigning a weight to each mRNA and miRNA for lncRNA by the integrative network. As a result, each lncRNA could be represented as a vector of these weights whose dimension equals the number of mRNAs and miRNAs in the network. Finally, the cosine similarity between vectors after using ITM Probe, which was implemented for calculating disease similarity in recent research [49], was exploited to calculate similarity of lncRNAs.

Figure 5: Overview of IntNetLncSim demonstrating the basic ideas of measuring lncRNAs functional similarity.

ITM Probe [48] is a tool for analyzing information flow in the network based on random walk with damping. Three models including absorbing, emitting, and channel were implemented in ITM Probe. Given a set of information sinks, the absorbing mode returns for any network node the likelihood of a random walk starting at that node to terminate at sinks. The emitting mode returns for each network node the expected number of visits to that node by a random walk starting at information sources. However, the directed flow from origins to destinations was induced via a potential function that was heuristic. Fortunately, channel model extends the absorbing model and emitting mode for directed information flow. According to these three models, all the nodes in the network were classified as boundary nodes and transient nodes. The boundary nodes contain source nodes that the random walk starts from and sink nodes that the random walk dissipates or ends at. And the transient nodes are neither source nodes nor sink nodes. After assigning boundary nodes and transient nodes, weights between these nodes could be outputted by the ITM Probe.

In this study, channel model in ITM Probe was applied to the integrative network. In this network, lncRNAs are not connected to each other, but they are linked to the mRNAs or miRNAs that are associated with them. The mRNAs and miRNAs are connected based on their curated interactions. Therefore, lncRNAs in the network were specified as boundary nodes, and all the mRNAs and miRNAs were specified as transient nodes, and with a damping factor of 0.85 according to previous research [50]. To assign a weight to each transient node for lncRNA, we consider a given lncRNA as source node and sink node in the information flow. Assuming N mRNAs and M miRNAs exist in the integrative network, each lncRNA can be represented as (N+M)-dimension vector based on the ITM Probe. For a given lncRNA lnc1, the weight vector can be described as

$WVlnc1={w1,1,w1,2,...,w1,i,...,w1,N+M},$   (2)

where WVlncl means a weight vector of lncl, and wl,i represents the weight score of lnc1 on the ith dimension. Then, we modeled the functional similarity between lncRNA lnc1 and lnc2 by the cosine of their vectors as following:

$Sim(lnc1,lnc2)=∑i=1N+Mw1,i⋅w2,i∑i=1N+Mw1,i2∑j=1N+Mw2,j2.$   (3)

#### Method for predicting disease-related lncRNAs

Disease-related lncRNAs were predicted using RWR analysis [51]. RWR is a global network ranking algorithm. The random walker starts on one or several seed nodes and then randomly transits to neighboring nodes considering the probabilities of the edges between the two nodes. The random walker can also return to the seed node, whose probability is supposed as γ, and then RWR algorithm can be defined as follows:

$Pt+1=(1−γ)APt+γP0.$   (4)

Here, P0 denotes the initial probability vector. Pt is a vector in which the ith element indicates the probability of finding the walker at node i at step t. A is the column-normalized adjacency matrix of the LFSN. The algorithm was performed until the probability of all the nodes become stable, and was defined as P. This can be measured by the difference between Pt and Pt+1 (measured by the L1 norm) falling below 10-10.

In this study, we predicted disease-related lncRNAs based on the constructed LFSN. The workflow was shown in Figure 6. For a given disease, the known disease-related lncRNAs were considered as seed nodes, while the rest lncRNAs were regarded as candidate lncRNAs. The seed nodes were mapped to the LFSN and a lncRNA rank list was then obtained using RWR algorithm. Each lncRNA was assigned a probability value in the above ranked list. The top ranked lncRNAs would have higher probability to be associated with a given disease.

Figure 6: Flowchart of predicting disease-related lncRNAs.

## ACKNOWLEDGMENTS

This work was supported by the National Natural Science Foundation of China (Grant No. 61403111, 61502125, and 31500675).

## CONFLICTS OF INTEREST

The authors declare that they have no of interest.

### Author contributions

MZ, LC and JS conceived and designed the experiments. LC, HS, ZW, JS, YH, HY and CZ analyzed data. MZ, LC and HS wrote this manuscript. All authors read and approved the final manuscript.

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